
    UNITED STATES of America, v. Herbert L. BENDOLPH, Appellant at No. 01-2468 United States of America v. Julio Otero, Appellant at No. 02-2624
    Nos. 01-2468, 02-2624.
    United States Court of Appeals, Third Circuit.
    Argued Oct. 26, 2004.
    Reargued En Banc Feb. 23, 2005.
    Decided May 16, 2005.
    
      David R. Fine, Esq. (Argued), Marsha A. Sajer, Esq., Robert A. Lawton, Kirkpatrick & Lockhart Nicholson Graham LLP, Harrisburg, PA, Counsel for Appellants.
    Colm F. Connolly, United States Attorney, District of Delaware, Richard G. Andrews, Esq. (Argued), Office of the United States Attorney, Wilmington, DE, Counsel for Appellees at 01-2468.
    Thomas A. Marino, Esq., United States Attorney, Middle District of Pennsylvania, Theodore B. Smith, III, Esq. (Argued), William A. Behe, Esq., Office of the United States Attorney, Harrisburg, PA, Counsel for Appellees at 02-2624.
    Maureen Kearney Rowley, Esq., Chief Federal Defender, Eastern District of Pennsylvania, Helen Marino, Esq., Michael Wiseman, Esq., Office of the Federal Defender, Philadelphia, PA, Amicus Curiae supporting Appellants.
    Patrick L. Meehan, Esq., United States Attorney, Eastern District of Pennsylvania, Laurie Magid, Esq., Robert A. Zauzmer, Esq., Michael J. Bres-nick, Esq., Office of the United States Attorney, Philadelphia, PA, Amicus Curiae supporting Appellees.
    Before: SCIRICA, Chief Judge, SLOVITER, NYGAARD, ROTH, McKEE, RENDELL, BARRY, AMBRO, FUENTES, SMITH, FISHER, and VAN ANTWERPEN, Circuit Judges.
   OPINION OF THE COURT

VAN ANTWERPEN, Circuit Judge.

This en banc court is presented with two cases consolidated on appeal. In the first case, Herbert Bendolph appeals from an order of the District Court which dismissed his motion to vacate, set aside, or correct a sentence under 28 U.S.C. § 2255 (“ § 2255 motion”) as untimely. In the second case, Julio Otero appeals from an order of the District Court denying him appointed counsel for an ineffectiveness of counsel evidentiary hearing held pursuant to his § 2255 motion. The District Courts had jurisdiction over these matters pursuant to 28 U.S.C. §§ 1381 and 2255. Our jurisdiction arises under 28 U.S.C. §§ 1291 and 2255.

Both cases raise issues concerning whether, under the Anti-Terrorism and Effective Death Penalty Act of 1996 (“AEDPA”), courts may raise the timeliness of § 2255 motions sua sponte, and, if so, under what circumstances. Neither case falls within the summary dismissal period of Rule 4 of the Rules Governing Section 2255 Cases for the United States District Courts (“Rule 4 period”) because in both cases the government has filed answers that did not raise the AEDPA statute of limitations as a defense.

We asked the parties and amici to brief four main issues. First, may the government waive the AEDPA statute of limitations as a defense? Second, may a district court raise it sua sponte? Third, if so, at what stages in a habeas case may á district court raise the limitations issue? Fourth, may a district court still raise the issue even if the government concedes waiver?

For the reasons discussed herein, we answer the first, second, and fourth issues in the affirmative. As to the third, we answer by concluding that (i) during the Rule 4 period, after giving notice and an opportunity to respond, courts may raise the AEDPA statute of limitations issue sua sponte without analysis of prejudice; and (ii) after the Rule 4 period has ended, courts may continue to raise the AEDPA statute of limitations issue sua sponte, but only after providing, consistent with our prior decisions in Robinson v. Johnson, 313 F.3d 128 (3d Cir.2002), and Long v. Wilson, 393 F.3d 390 (3d Cir.2004), notice, an opportunity to respond, and an analysis of prejudice. Accordingly, we will affirm the District Court’s order in Bendolph. In Otero, we will reverse and remand to the District Court, with instructions to the District Court that it has discretion to raise the AEDPA limitations issue sua sponte.

I.

The relevant facts of these cases may be summarized as follows. A jury in the United States District Court for the District of Delaware convicted Herbert Ben-dolph of being a felon in possession of a firearm. We affirmed his conviction, 116 F.3d 470, entering judgment on May 5, 1997. The Delaware Federal Defender, acting as Bendolph’s counsel, then filed a petition with the Supreme Court of the United States for a writ of ceHiorari on August 25, 1997. Under Supreme Court Rule 13.1, which requires the filing of such petitions within 90 days of judgment, Ben-dolph’s petition was untimely. The Clerk of the Supreme Court was unaware of this, however, because someone involved in the filing of the petition impermissibly altered the date of this Court’s judgment. On the copy filed with the Supreme Court, someone had typed the number “27” over the “5” in the judgment date of May 5, 1997. As a result, the Clerk of the Supreme Court mistakenly believed the petition for ceHiorari was timely.

A year later, on October 18, 1998, Ben-dolph filed a pro se motion under 28 U.S.C. § 2255. This too was untimely: Bendolph was obligated under the AEDPA’s one-year statute of limitations to have filed his motion by August 4, 1997, one year from the date on which the 90 day period to file a petition for ceHiorari had ended. See U.S.Supr. Ct. R. 13; Kapral v. United States, 166 F.3d 565, 575, 577 (3d Cir.1999) (holding that a judgment may become “final” in the context of §§ 2254 and 2255 when “the date on which the defendant’s time for filing a timely petition for ceHio-rari review expires”). Two weeks after Bendolph filed his § 2255 motion, the District Court ordered the government to file an answer. It did so on December 17, 1998, and did not raise the AEDPA limitations defense. Eight months later, the District Judge retired, and the matter was reassigned to another District Judge.

One year later, on August 24, 2000, the District Court entered an order suggesting the case was untimely under our decision in Kapral, 166 F.3d at 575-77, given that Bendolph had not timely filed a petition for certiorari by August 4, 1997, or 90 days after our May 5, 1997 judgment. In its August 24, 2000 order, the District Court identified the reasons why the case appeared to be time-barred, invited the parties to brief the issue, and set a deadline of September 21, 2000 for Bendolph to respond to the District Court’s analysis. Bendolph filed a three-page memorandum almost two weeks before that deadline, on September 8, 2000. The government responded on October 5, 2000, agreeing with the District Court that the case was time-barred. The District Court subsequently dismissed Bendolph’s § 2255 motion as untimely on January 3, 2001. Now, on appeal, Bendolph argues the District Court lacked the authority to raise the ÁEDPA limitations period sua sponte because the government had waived the defense by not raising it in its answer.

In the second ease, Julio Otero pled guilty to operating a continuing criminal enterprise in violation of 21 U.S.C. § 848(a). On May 27, 1998, the United States District Court for the Middle District of Pennsylvania sentenced him to life imprisonment.. In accordance with his plea agreement, Otero did not appeal his conviction. On June 25, 2001, Otero filed a pro se § 2255 motion challenging the validity of his sentence on several grounds, including ineffective assistance of counsel. The government filed its answer on September 17, 2001. It did not raise the AEDPA’s statute of limitations as a defense.

The District Court initially denied all of Otero’s claims except his ineffective assistance of counsel claim, for which an evi-dentiary hearing was scheduled. The District Court did not appoint counsel to represent Otero at that hearing, and denied his claim on the merits. Otero argues on appeal that (i) the District Court erred in failing to appoint counsel for him at his evidentiary hearing, and (ii) neither the District Court nor the government may raise the AEDPA statute of limitations issue on remand because the government has waived the defense.

II.

We turn first to the District Court’s decision not to provide counsel to Otero at his ineffective assistance of counsel evidentiary hearing. Rule 8(c) of the Rules Governing Section 2255 Cases requires that “[i]f an evidentiary hearing is warranted, the judge must appoint an attorney to represent a moving party who qualifies to have counsel ... [as an indigent].” The appointment of counsel is clearly mandatory for an indigent petitioner. See United States v. Iasiello, 166 F.3d 212, 213-14 (3d Cir.1999) (vacating judgment and remanding to district court where district court conducted a § 2255 evidentiary hearing without appointing counsel to indigent movant). “[H]arm to [a movant] must be presumed when his statutory right to counsel is thus abridged.” Id. at 214. The government does not dispute that, as a federal inmate since 1996, Otero is likely indigent; nor does it attempt to rebut the presumption of prejudice. Accordingly, we must reverse the District Court’s dismissal of Otero’s ineffective assistance of counsel claim. The record is unclear as to whether Otero is indigent and the -District Court should inquire as to his status. Should he qualify as indigent, he must be afforded counsel for his ineffective assistance of counsel claim.

III.

A.

We now turn to the four main issues, supra, before us in these consolidated appeals. The analysis of the AEDPA statute of limitations issue, which in these two cases involves undisputed facts, is subject to plenary review. See, e.g., Long, 393 F.3d at 396 (citing Swartz v. Meyers, 204 F.3d 417, 419 (3d Cir.2000)); see also Werts v. Vaughn, 228 F.3d 178 (3d Cir.2000).

As we observed in Long, our analysis necessarily begins with Robinson, 313 F.3d 128. Our prior discussion of that case in Long is thorough, see 393 F.3d at 396-98, and needs no further elaboration here. In Long we encapsulated Robinson ’s holdings as follows:

[F]irst ... because the statute of limitations is not jurisdictional in nature, see Miller v. New Jersey State Dep’t of Corr., 145 F.3d [616], 617-18 [ (3d Cir.1998) ], the state may waive the defense .... [W]e then considered whether Federal Rule of Civil Procedure 8(c) requires that a defendant plead ... a statute of limitations[ ] in its answer.... We explained: “Parties are generally required to assert affirmative defenses early in litigation, so ... prejudice may be avoided[ ] and judicial resources may be conserved. Habeas proceedings are no exception.” ... We further emphasized: “The purpose ... is to avoid surprise and undue prejudice by providing the plaintiff with notice and the opportunity to demonstrate why the affirmative defense should not succeed.”....
[We then] held that “a limitations defense does not necessarily have to be raised in the answerf,]” [but] must be raised “as early as practicable” thereafter.... What the earliest practicable or possible or feasible moment might be in another case ... we necessarily left open.

Long, 393 F.3d at 397-98 (quoting Robinson, 313 F.3d at 134-37). Consistent with these holdings, we then analyzed in Long a Magistrate Judge’s report and recommendation that flagged the limitations issue sua sponte. We used the analytical framework provided by Federal Rule of Civil Procedure 15(a) because the government had subsequently filed, in response, an “endors[ment] [of] the Magistrate Judge’s view that the habeas petition was untimely.” Long, 393 F.3d at 395. Under Rule 15(a), we articulated a standard for judging prejudice in the AEDPA statute of limitations context as follows:

[ Our prior cases including Robinson ] counsel that, whether a habeas petitioner has been prejudiced by the assertion of the AEDPA statute of limitations defense after an answer has been filed is the ultimate issue, and that prejudice turns on such factors as how late in the proceedings the defense was raised, whether the petitioner had an opportunity to respond, and whether the respondent acted in bad faith .... Delay is related to prejudice but was not a problem here, and inadvertence does not equal bad faith.

Id. at 401 (internal citations omitted). We held that Long was not prejudiced by the government’s delay in raising the limitations defense, which it had done through its express endorsement of the Magistrate Judge’s analysis of the timeliness issue. We then concluded that the District Court did not abuse its discretion by construing the government’s filing as an amendment to its answer. Id. at 401.

Addressing the Magistrate Judge’s sua sponte flagging of the limitations issue, we said:

Our answer to [this issue] was foreshadowed by Banks v. Horn, 271 F.3d 527, 533 n. 4 (3d Cir.2001), rev’d on other grounds, 536 U.S. 266, 122 S.Ct. 2147, 153 L.Ed.2d 301 (2002) .... In a footnote ... we expressed the view that a court of appeals could address the AED-PA statute of limitations defense sua sponte even if the habeas respondent had waived the issue on appeal. We wrote:
“Even if not raised, we believe we could consider the issue sua sponte .... The Court has the power to notice a ‘plain error’ though it is not assigned or specified .... In exceptional circumstances, especially in criminal cases, appellate courts, in the public interest, may, of their own motion, notice errors to which no exception has been taken, if the errors are obvious, or if they otherwise seriously affect the fairness, integrity or public reputation of judicial proceedings.”
Thus we observed prior to Robinson that the AEDPA statute of limitation is an important issue, the raising of which may not necessarily be left completely to the state.

Long, 393 F.3d at 401-02 (quoting Banks, 271 F.3d at 533 n. 4) (internal citations and quotations omitted). After then reviewing the relevant decisions of the other courts of appeals, especially Acosta v. Artuz, 221 F.3d 117 (2d Cir.2000), we held further that

our decision in Robinson ... does not prevent a magistrate judge from raising the AEDPA statute of limitations defense sua sponte even after an answer has been filed.

Long, 393 F.3d at 403 (internal citations omitted).

Fundamental to our analysis was (i) our agreement with the Second Circuit that “[w]hile civil in nature, habeas corpus cases are different from ordinary civil cases where only the interests of the parties are involved,” Long, 393 F.3d at 402 (citing Acosta, 221 F.3d at 123), and (ii) our conclusion that courts “may raise the ... limitations issue ... after an answer has been filed.” Long, 393 F.3d at 403. Our basis for the latter was Granberry v. Greer, 481 U.S. 129, 134-35, 107 S.Ct. 1671, 95 L.Ed.2d 119 (1987) (holding courts have discretion, in interests of comity and federalism, to require that a claim be fully exhausted or to reject it if it plainly lacks merit), as well as our prior decisions in cases such as Sweger v. Chesney, 294 F.3d 506, 520-21 (3d Cir.2002) (holding courts may consider sua sponte whether procedural default bars claim), cert. denied, 538 U.S. 1002, 123 S.Ct. 1902, 155 L.Ed.2d 830 (2003) and Szuchon v. Lehman, 273 F.3d 299, 321 n. 13 (3d Cir.2001) (holding court of appeals can sua sponte consider procedural default). See Long, 393 F.3d at 402-403.

We rejected two decisions contra, Scott v. Collins, 286 F.3d 923 (6th Cir.2002) and Nardi v. Stewart, 354 F.3d 1134 (9th Cir.2004), concluding they were “at odds with Robinson and our Rule 15(a) jurisprudence, which do not require that affirmative defenses be pled in the first responsive pleading.” Long, 393 F.3d at 403. We then stated that:

[ hjaving in mind that AEDPA’s statute of limitations, like other procedural ha-beas issues, furthers the principles of comity, finality, and federalism, ... we hold further that a federal magistrate judge may, consistent with Robinson v. Johnson ... raise sua sponte the AED-PA statute of limitations defense even after an answer has been filed.

Long, 393 F.3d at 404 (internal citations omitted).

With the analytical framework of Robinson and Long in mind, we turn to the questions before us.

B.

We must first address whether our decisions in the Long and Robinson § 2254 cases apply to the § 2255 cases before us today. In resolving the question, we are mindful of our obligation to be faithful to the intent of Congress’ 1996 habeas corpus reforms. Congress was cognizant not just of the practical realities of habeas filings, but also the spectrum of federal interests that those realities implicate, as evidenced by “the profound societal costs that attend the exercise of habeas jurisdiction.” Calderon v. Thompson, 523 U.S. 538, 554, 118 S.Ct. 1489, 1500, 140 L.Ed.2d 728 (1998) (internal quotation omitted) (emphasis added). “ ‘AEDPA’s purpose” ’ is not only to further the interests of comity and federalism, but also to further the “ ‘finality’ ” of convictions, Duncan v. Walker, 533 U.S. 167, 178, 121 S.Ct. 2120, 2127, 150 L.Ed.2d 251 (2001) (quoting Williams v. Taylor, 529 U.S. 420, 436, 120 S.Ct. 1479, 1490, 146 L.Ed.2d 435 (2000)), and to curb abusive habeas filings. See, e.g., H.R. Conf. Rep. No. 104-518, at 111 (1996), reprinted in 1996 U.S.C.C.A.N. 944 (stating that AED-PA was passed, in relevant part, “to curb the abuse of the statutory writ of habeas corpus”). Other courts have similarly held that “a signal purpose[] animating AEDPA is the desire of Congress to achieve finality in criminal statutes, both federal and state.” Brackett v. United States, 270 F.3d 60, 69 (1st Cir.2001) (citations omitted), cert. denied, 535 U.S. 1003, 122 S.Ct. 1575, 152 L.Ed.2d 495 (2002). See also United States v. Espinoza-Saenz, 235 F.3d 501, 505 (10th Cir.2000) (noting the “intent of Congress that claims under § 2255 be advanced within one year after a judgment of conviction becomes final”) (internal citations omitted).

We have similarly recognized the wide spectrum of interests that Congress intended to protect through habeas reform. See, e.g., Long, 393 F.3d at 402-03 (identifying interests of judicial economy and finality of judgments in concluding that “[tjhe AEDPA statute of limitations is an important issue, the raising of which may not necessarily be left completely to the state”); Robinson, 313 F.3d at 137 (recognizing an interest in not “wasting precious legal and judicial resources”). See also United States v. Brooks, 230 F.3d 643, 649 (3d Cir.2000) (observing Congress’ intent in amending § 2255 was “to place limits on federal collateral review”); Banks, 271 F.3d at 533 n. 4 (recognizing interests of, inter alia, the public reputation of judicial proceedings and the public interest generally); Kapral, 166 F.3d at 571 (recognizing “Congress[’] inten[t] to reduce ... delayed and repetitive [habeas] filings”) (internal quotation omitted); Miller, 145 F.3d at 618 (stating that the AEDPA “was enacted, in relevant part, to curb the abuse of the writ of habeas corpus.”) (emphasis in original).

It is thus clear, we believe, that Congress’ intent with respect to habeas reform — one facet of which is the AEDPA statute of limitations — was not limited to interests of federalism and comity, which apply only to petitions filed under § 2254. Rather, Congress was concerned with abuses of, and the interests implicated by, habeas filings under both §§ 2254 and § 2255.

Second, to provide guidance to the district courts, as well as to avoid confusion, we have previously held that we should treat § 2255 motions and § 2254 petitions the same absent sound reason to do otherwise. See, e.g., Miller, 145 F.3d at 619 n. 1 (“[T]o provide guidance to the. district courts, and hence facilitate the orderly administration of justice in these cases, we have followed the practice, whenever we decide an AEDPA issue that arises under § 2254 and the same holding would analytically be required in a case arising under § 2255, or vice versa, of so informing the district courts.”). We see no reason to depart from this practice here.

Third, such an approach is consistent with the interests served by statutes of limitations generally. Limitations periods “protect defendants and the courts ... United States v. Kubrick, 444 U.S. 111, 117, 100 S.Ct. 352, 357, 62 L.Ed.2d 259 (1979) (internal quotation omitted) (emphasis added), because they “free[ ] ... courts from adjudicating stale claims,” Sun Oil Co. v. Wortman, 486 U.S. 717, 736, 108 S.Ct. 2117, 2129, 100 L.Ed.2d 743 (1988) (Brennan, J., concurring). They also support “ ‘the minimization of unnecessary litigation.’ ” Felder v. Casey, 487 U.S. 131, 154, 108 S.Ct. 2302, 2315, 101 L.Ed.2d 123 (1988) (White, J., concurring) (internal quotation omitted). These public and judicial interests transcend the parties to a litigation in the same way as the interests furthered by the AEDPA’s limitations period. See Long, 393 F.3d at 402-04; Robinson, 313 F.3d at 134-37; Banks, 271 F.3d at 533 n. 4; Artuz, 221 F.3d at 123.

Because there exist sound reasons to approach the AEDPA limitations period the same under both §§ 2254 and 2255, and because to do so is faithful with both Congress’ intent and our habeas jurisprudence, we hold that our § 2254 decisions in Robinson and Long apply to AEDPA limitations issues arising under § 2255.

C.

We return to the four main issues we asked the parties and amici to brief.

(1) With regard to the government’s ability to waive the AEDPA statute of limitations, all of the parties and both amici agree that, under our decisions in Miller, Robinson, and Long, discussed supra, the limitations period is not jurisdictional and therefore is subject to equitable considerations such as waiver. We accordingly reaffirm our holdings on these issues in these cases.

The more difficult question, which we address infra, remains: whether a party’s waiver of a defense, intentional or not, may impact the exercise of an inherent power that a court may possess in the circumstances presented here. We foreshadow our answer by observing that neither the parties nor amici have cited to us authority requiring that a party’s waiver of a defense must necessarily curtail the inherent powers of a court.

(2) As to the second main issue, whether courts ever have the power to act sua sponte in the circumstances here, the answer is plainly yes. First, as we have discussed supra, the eases confirm, in similar contexts, an analogous power. See, e.g., Granberry, 481 U.S. at 134-35, 107 S.Ct. 1671, 95 L.Ed.2d 119; Sweger, 294 F.3d at 520-21; Szuchon, 273 F.3d at 321 n. 13. This authority is persuasive with respect to the issue before us because we have already recognized that the AEDPA statute of limitations is “like other procedural habeas issues.” Long, 393 F.3d at 404. The application of such cases to the circumstances before us also conforms with sua sponte jurisprudence generally.

Second, while two circuits disagree with our conclusion in Long as to when a court may act sua sponte, all of the courts of appeals that have considered the issue agree that courts do possess a sua sponte power to raise the limitations issue. See, e.g., Hill v. Braxton, 277 F.3d 701, 705-06 (4th Cir.2002) (“Even though the limitations period is an affirmative defense, a federal habeas court has the power to raise affirmative defenses sua sponte .... We agree with our sister circuits that have determined a district court has the power to raise the limitations defense [to a § 2254 petition] sua sponte.”); Jackson v. Sec’y for the Dep’t of Corr., 292 F.3d 1347, 1349 (11th Cir.2002) (per curiam) (“we hold that the district court possessed the discretion to raise sua sponte the timeliness issue”); Artuz, 221 F.3d at 124 (holding “a district court has the authority to raise the AEDPA statute of limitations on its own motion”); Kiser v. Johnson, 163 F.3d 326, 329 (5th Cir.1999) (“In holding that Fed. R.Civ.P. 8(c) does not bar sua sponte consideration of the AEDPA’s statute of limitations provision, we follow a long line of precedent establishing the authority of courts to raise non-jurisdictional defenses sua sponte in habeas cases.”). See also United States v. Sosa, 364 F.3d 507, 510 (4th Cir.2004) (applying Hill to motion filed under § 2255).

The decisions contra to our decision in Long with respect to when a district court may sua sponte raise the limitations issue do not suggest that courts lack the inherent power in the first place. See Herbst v. Cook, 260 F.3d 1039, 1042 (9th Cir.2001) (“The district court ... had the authority to raise the [AEDPA] statute of limitations sua sponte.”); Nardi v. Stewart, 354 F.3d 1134, 1141 (9th Cir.2004) (reaffirming Herbst’s holding that a district court may raise sua sponte the limitations defense, but narrowing the time period in which the court can do so); Scott v. Collins, 286 F.3d 923, 930 (6th Cir.2002) (holding Rule 4 does not give a district court “continuing” power to dismiss sua sponte after the Rule 4 period ends).

As we discussed supra and first articulated in Long, the interests underlying the AEDPA’s statute of limitations that are applicable to § 2255 motions are furthered, not hindered, by courts exercising discretionary power sua sponte in post-answer cases such as those before us here. See Long, 393 F.3d at 402-03 (identifying interests of judicial economy and finality of judgments); Robinson, 313 F.3d at 137 (identifying “precious legal and judicial resources”). See also Banks, 271 F.3d at 533 n. 4 (recognizing the public reputation of judicial proceedings and the public interest generally); Kapral, 166 F.3d at 571 (recognizing “Congress[’] inten[t] to reduce ... delayed and repetitive [habeas] filings”) (internal quotation omitted).

Finally, we consider the argument contra, a thumbnail sketch of which is this: Habeas cases are civil, governed by the Federal Rules of Civil Procedure. As such, the AEDPA statute of limitations must be treated like any other in a civil case. Therefore, it is a defense possessed by the habeas respondent alone, and courts may not intervene.

The argument plainly rests on the premise that habeas cases and ordinary civil cases are indistinguishable, something we disagreed with in Long and do so again today. See, e.g., Harris v. Nelson, 394 U.S. 286, 293-94, 89 S.Ct. 1082, 1087-88, 22 L.Ed.2d 281 (1968) (“It is, of course, true that habeas corpus proceedings are characterized as ‘civil.’ ... But the label is gross and inexact. Essentially, the proceeding is unique. Habeas corpus practice in the federal courts has conformed with civil practice only in a general sense.”) (internal citations and footnote omitted); Long, 393 F.3d at 402 (“While civil in nature, habeas corpus cases are different from ordinary civil cases where only the interests of the parties are involved.”) (citing Acosta, 221 F.3d at 123); see also O’Brien v. Moore, 395 F.3d 499, 505 (4th Cir.2005) (noting the unique hybrid nature of habeas actions and collecting cases observing same); Walker v. O’Brien, 216 F.3d 626, 636 (7th Cir.2000) (observing that habeas cases are a “group unto themselves”); Brown v. Vasquez, 952 F.2d 1164, 1169 (9th Cir.1991) (noting habeas corpus is “dramatically different from any other type of civil action”).

As to the claim that the AEDPA statute of limitations is the government’s alone to use or lose, we have found no authority supporting such exclusivity. Certainly, we have been cited to none. As such, we must doubt that Congress intended to relegate the efficacy of its reforms to the vagaries of a prosecutor’s decisions or mistakes. Similarly, we discern no Congressional intent to hamstring courts in carrying out its reforms. The better conclusion is that Congress did not render the courts powerless.

For all of these reasons, we reaffirm Long and hold that courts have the power to raise the AEDPA limitations issue sua sponte in cases arising under 28 U.S.C. §§ 2254 and 2255.

(3) What remains are our final two main issues and their application to the cases before us. For analytical purposes, they may be combined: Given the courts’ power to raise the AEDPA statute of limitations sua sponte, at what stages may they do so, and does it matter if the government has waived?

We hold the answer is once again provided by our decision in Long. Our analysis there presents no obvious reason why, given notice and an opportunity to respond, and absent prejudice to the habeas petitioner or movant, a court’s exercise of its sua sponte powers should be limited to only the Rule 4 period. The spectrum of interests that we identify in Robinson, Long, and this opinion today — finality and judicial efficiency, most notably, but also the public interest and the public reputation of judicial proceedings — are just as ably advanced post-answer as pre-answer when an untimely case is dismissed upon a district court’s own motion. Recognition of this disentangles the overriding federal, judicial, and societal interests that are relevant to our analysis from those that concern the parties alone. Further, as we have stated, such an approach is not only most faithful to Congress’ 1996 habeas reforms, but it is also most certainly not inconsistent with existing authority. We have been cited to nothing that requires the inherent sua sponte power to terminate at the conclusion of the Rule 4 period, and we can find no such authority ourselves.

The above considerations, which we fully articulated in Long, are no less persuasive in instances where the government has either waived the limitations defense or so concedes. Not only are habeas cases different, but, as for the AEDPA limitations provision, the government can claim no monopoly on its use.

To conclude otherwise asks too much of waiver, which occurs only upon the “ ‘intentional relinquishment or abandonment of a known right.’ ” United States v. Olano, 507 U.S. 725, 733, 113 S.Ct. 1770, 1777, 123 L.Ed.2d 508 (1993) (quoting Johnson v. Zerbst, 304 U.S. 458, 464, 58 S.Ct. 1019, 1023, 82 L.Ed. 1461 (1938)). Unlike ordinary civil litigation, the practical reality of habeas is that the government may lack, for long periods of time, the file documents necessary to knowledgeably analyze timeliness. As amicus Federal Defender observes, habeas cases present “sometimes difficult questions of time computation.” Brief of Amicus at 13. Indeed, the Supreme Court has explained:

[District judges often will not be able to make [AEDPA limitations] calculations based solely on the face of habeas petitions .... [As] [s]uch calculations depend on information contained in documents that do not necessarily accompany the petitions.

Pliler v. Ford, 542 U.S. 225, 124 S.Ct. 2441, 2446, 159 L.Ed.2d 338 (2004) (citation omitted). The result is that, all too easily, habeas respondents and courts may “err in their calculation ....” Id. at 2447. Even when the record papers are obtained, it can be difficult to decipher what a pro se habeas movant has done, meaning many “waivers” will not actually have been “the result of a purposeful or deliberate decision to forego the defense.” Scott, 286 F.3d at 931 (Stafford, J., dissenting). For these reasons and others, Long correctly instructs that the analysis in the first instance turns not. on waiver, but rather on whether courts have the inherent power to protect themselves from ha-beas abuse, post-answer, consistent with Congress’ intent, and whether, where a court exercises that power, the habeas movant is prejudiced.

(4) With these' precepts in mind, we turn to the cases before us. In Bendolph, a judgment entry of this Court was intentionally and impermissibly altered by someone involved in filing Bendolph’s petition for a writ of certiorari, to conceal the untimeliness of a Supreme Court filing. Such an act should not, of course, be countenanced in any way. Without doubt, the ability of a court to, deal with such a circumstance is inherently within its sua sponte powers, and does not depend on the responding party’s position.

The issue before us, however, is whether the District Court could raise the AEDPA limitations issue on its own motion, and, if so, whether the exercise of that power was limited by a government waiver. For the reasons we have discussed above, we conclude that the District Court did possess the power to flag the issue sua sponte, and that even if the government’s actions did constitute waiver, that waiver could not have limited the court’s exercise of its power.

The questions remaining are (i) whether the District Court provided Bendolph with adequate notice of the issue and an opportunity to respond, and (ii) whether Bendolph was prejudiced by the District Court’s motion. The record shows that the District Court’s August 24, 2000 order placed both Bendolph and the government on notice, both by raising the timeliness issue and by articulating the reasons why Bendolph’s filing appeared untimely. In that same order, the District Court expressly invited the parties to brief or otherwise respond to its analysis. Bendolph was given until September 21, 2000 to respond. That the District Court’s order constituted sufficient notice and provided sufficient time and opportunity to respond is evidenced by the fact that Bendolph filed his memorandum in response two weeks early, on September 8, 2000. The District Court subsequently received a letter submission from the government on October 5, 2000. It then denied Ben-dolph’s § 2255 motion as untimely about three months later, on January 3, 2001. On these facts, we hold that Bendolph was provided adequate notice of the timeliness issue, as well as adequate opportunity to respond.

Because the District Court flagged timeliness after the Rule 4 period had ended, we must next consider “the ultimate issue,” prejudice to Bendolph. Long, 393 F.3d at 401. We look first to how late in the case the limitations issue was raised. Id. Here, as stated, the District Court raised the issue on August 24, 2000; the government, in turn, did so on October 5, 2000. These two events occurred almost two years after October 18, 1998, the date Bendolph filed his § 2255 motion. During that time, the record reflects the following activity in-Bendolph’s case: he filed a motion to compel discovery, which was denied; the case was reassigned upon the retirement of the District Judge; and Ben-dolph was ordered to make an election pursuant to United States v. Miller, 197 F.3d 644 (3d Cir.1999). On these facts, the raising of timeliness was not so late that Bendolph was prejudiced. There is no evidence that he had .commenced costly or time-consuming discovery, suffered a loss or a diminution of his ability to prepare his case, or lost another litigation opportunity elsewhere. As such, while “[djelay is related to prejudice,” and while a period of almost two years may be strong evidence of prejudice in another case, “[it] was not a problem here.” Long, 393 F.3d at 401. The prejudice inquiry looks next to whether Bendolph had sufficient opportunity to respond to the issue, once raised. See id. We have already discussed this in our analysis of notice; such opportunity was plain from the District Court’s August 24, 2000 order and Bendolph’s memorandum in response. There is no problem here, either. Finally, we consider whether the government acted in bad faith. Just as it would be unfair to ascribe the altered judgment entry date to Bendolph himself, rather than someone acting on his behalf, it would also be unfair to suggest that the government’s delay was improper. See Long, 393 F.3d at 401 (“[ijnadvertence does not equal bad faith”).

No prejudice arising from the District Court’s sua sponte flagging of the issue, and notice and an opportunity to respond having been shown on this record, we affirm the District Court’s dismissal of the § 2255 motion in Bendolph as untimely.

This leaves Otero. We have already reversed and remanded for failure to appoint counsel, as discussed supra. As to the remaining issue of whether the District Court may consider the apparent untimeliness of Otero’s § 2255 motion sua sponte on remand, we answer in the affirmative, provided the District Court gives notice, an opportunity to respond, and a prejudice analysis consistent with this opinion and our prior decision in Long. ,

D.

In conclusion, we hold that, upon finding a potential AEDPA statute of limitations problem in a habeas case arising under 28 U.S.C. §§ 2254 or 2255, a court may act sua sponte at any point in the proceedings, regardless of the government’s position, provided the court (i) gives notice of the issue and an opportunity to respond; and, (ii) if the case has passed the Rule 4 stage, also analyzes the prejudice components of Rule 15(a) and Long that we reaffirm today. The application of these mandatory requirements, like the determination of timeliness itself, remains subject to plenary review. See Long, 393 F.3d at 396. What remains, including whether to raise timeliness sua sponte in the first place, and, if so, whether to invite the government to amend its answer or not, remains within the district courts’ sound discretion and will not be disturbed absent an abuse of that discretion. Id.

For the foregoing reasons, the January 3, 2001 order of the District Court dismissing the § 2255 motion of Herbert Ben-dolph is affirmed, and the February 4, 2002 order of the District Court dismissing the § 2255 motion of Julio Otero and denying his ineffectiveness of counsel claim is reversed and remanded to the District Court for further proceedings consistent with this opinion.

NYGAARD, Circuit Judge,

with whom Judges SLOVITER, MCKEE, AMBRO and FUENTES join, concurring in part and dissenting in part.

I concur with the majority that we must reverse the dismissal of Otero’s ineffective assistance of counsel claim and remand for the District Court to decide whether Otero is indigent and qualifies for appointed counsel. I concur with the majority that, subject to notice and an opportunity to be heard, a district court may dismiss a habe-as petition sua sponte as part of its preliminary consideration pursuant to Rule 4 of the rules governing both section 2254 and section 2255 cases. I also concur with the majority that the one year statute of limitations contained in the Antiterrorism and Effective Death Penalty Act, 28 U.S.C. §§ 2244(d)(1), 2255, is subject to waiver as a defense by the government. See Robinson v. Johnson, 313 F.3d 128, 134 (3d Cir.2002). But thereafter the majority and I part company. I dissent from the majority’s holding that a district court has the authority to raise AEDPA’s statute of limitations sua sponte after the government has failed to raise that affirmative defense in its answer to the petition.

I.

As an initial matter, I would remand Bendolph’s petition for a factual finding on the equitable tolling claim he raised on appeal. As explained by the majority, the Clerk of the Supreme Court mistakenly filed Bendolph’s untimely petition for cer-tiorari because the date on the copy of our judgment entry had been altered, making the petition appear timely. Because the Clerk did not reject his certiorari petition as untimely, Bendolph believed, in error, that AEDPA’s statute of limitations did not begin to run on his habeas petition until one year from the date the Supreme Court denied certiorari. Bendolph, therefore, did not file his habeas petition within one year of the date his conviction actually became final as AEDPA requires. See 28 U.S.C. § 2255. On appeal before the panel, he argued that the mistaken filing of his certiorari petition by the Clerk of the Supreme Court is grounds for equitable tolling of AEDPA’s statute of limitations. Because it is unclear who altered the record, we cannot know whether equitable tolling is appropriate and we should remand for further factual findings.

AEDPA’s statute of limitations is subject to equitable tolling. Fahy v. Horn, 240 F.3d 239, 244 (3d Cir.2001). Out of a sense of equity, we will toll the statute of limitations when a petitioner demonstrates reasonable diligence in bringing a claim, but “has in some extraordinary way been prevented from asserting his or her rights.” Miller v. New Jersey State Dep’t of Corr., 145 F.3d 616, 618. In non-capital cases, “attorney error, miscalculation, inadequate research, or other mistakes have not been found [by this Court] to rise to the ‘extraordinary’ circumstances required for equitable tolling.” Fahy, 240 F.3d at 244. We have also held, however, that there are “narrow circumstances in which misbehavior of an attorney may merit such equitable relief.” Seitzinger v. Reading Hosp. & Med. Cent., 165 F.3d 236, 239 (3d Cir.1999). For instance, in Nara v. Frank, 264 F.3d 310, 320 (3d Cir.2001), a habeas petitioner accused his attorney of leading him to believe that the attorney would file a habeas petition on his behalf, and of telling him that there were no time constraints on habeas petitions. Id. We found that, if true, the allegations “may constitute extraordinary circumstances to justify equitable tolling.” Id. Nevertheless, because the Court was unable to determine the validity of the accusations, it remanded for a factual finding. Id.

Like in Nora, a remand is presently appropriate. Although it is unclear who altered the date on this Court’s judgment entry, the alteration misled the Clerk of the Supreme Court to believe that Ben-dolph’s petition for certiorari was timely. It is entirely possible that the alteration is the result of clerical error. Indeed, there is no evidence in the record that Ben-dolph’s federal public defender altered the document herself, innocently or otherwise. Nor is there evidence that she purposefully or knowingly submitted an altered document to the Clerk of the Supreme Court. If the federal public defender altered the document, her actions would be sufficiently serious to constitute an “extraordinary” prevention of Bendolph’s ability to assert his rights that would merit equitable tolling. I believe it patently unfair of the majority to acknowledge the altered date and then simply affirm the District Court without permitting Bendolph the opportunity to show that he was misled into believing he had time to file his habeas petition. Because the record does not permit us to determine who is responsible for the alteration, we should remand for the District Court to make factual findings, and for it to determine whether the statute of limitations should be tolled. Under these circumstances, there is a possibility that Bendolph’s petition was indeed timely.

II.

In the event the petitions were untimely, Rule 5(b) of the Rules Governing Section 2254 Cases in the United States District Courts requires that an answer to a habe-as petition “must state whether any claim in the petition is barred by a failure to exhaust state remedies, a procedural bar, non-retroactivity, or a statute of limitations.” Section 2254 Rule 5(b) (emphasis added). The phrase “statute of limitations” was added to Rule 5(b) in December 2004 as part of a “stylistic” change meant to reflect the existing state of the law. See Section 2254 Rule 5, cmt.

At the time of the amendment, the Courts of Appeals for the Sixth, Ninth, and Eleventh Circuits had addressed the effect of the government’s failure to raise the AEDPA statute of limitations in its answer on a district court’s authority to subsequently raise the issue sua sponte. In Scott v. Collins, 286 F.3d 923, 927 (6th Cir.2002), the Sixth Circuit held that because AEDPA’s statute of limitations is an affirmative defense, “Rule 8(c) of the Federal Rules of Civil Procedure requires that [the government] raise it in the first responsive pleading to avoid waiving it.” The Court held that the government’s failure to raise the statute of limitations in its answer divests the district court of its authority to raise the defense sua sponte. Id. at 930. It explained that a contrary rule would amount to “an impermissible curing of [the government’s] waiver.” Id. The Ninth Circuit applied similar reasoning in Nardi v. Stewart, 354 F.3d 1134 (9th Cir.2004). It held that a “district court lacks the authority to sua sponte dismiss a habeas petition as time-barred after the state files an answer which fails to raise the statute of limitations defense.” Id. at 1141. By contrast, the Eleventh Circuit, in Jackson v. Secretary for the Department of Corrections, 292 F.3d 1347, 1349 (11th Cir.2002), held without any analysis that the government’s failure to raise the statute of limitations in its answer has no effect on a district court’s ability to raise the issue sua sponte. Thus, at the time of this Court’s decision in Long v. Wilson, 393 F.3d 390 (3d Cir.2004), there existed a circuit split. In Long, we sided with the Eleventh Circuit, id. at 403, and today the majority reaffirms that choice, albeit in the context of a section 2255 petition rather than a section 2254 petition. We are on the wrong side of the split between the circuits.

Underlying the Scott and Nardi decisions is the rule that generally it is not appropriate for a court to sua sponte raise non-jurisdictional defenses not raised by the parties. See Acosta v. Artuz, 221 F.3d 117, 122 (2d Cir.2000) (“Generally, courts should not raise sua sponte nonjurisdic-tional defenses not raised by the parties.”); cf. Zelson v. Thomforde, 412 F.2d 56, 58 (3d Cir.1969) (holding that a court may not raise the defense of lack of personal jurisdiction — a non-jurisdictional defense because it does not concern the power of the court to entertain the suit — once the defendant has waived the issue by appearing). This rule exists because ours is an adversarial system, which relies on advocacy by trained counsel. Cf. United States v. Burke, 504 U.S. 229, 246, 112 S.Ct. 1867, 119 L.Ed.2d 34 (1992) (Scalia, J., concurring) (“The rule that points of law not argued will not be considered is more than just a prudential rule of convenience; its observance, at least in the vast majority of cases, distinguishes our adversary system of justice from the inquisitorial one.”). In an adversarial system, it is not for the courts to bring to light the best arguments for either side; that responsibility is left to the parties themselves. McNeil v. Wisconsin, 501 U.S. 171, 181 n. 2, 111 S.Ct. 2204, 115 L.Ed.2d 158 (1991) (“What makes a system adversarial rather than inquisitorial is ... the presence of a judge who does not (as an inquisitor does) conduct the factual and legal investigation himself, but instead decides on the basis of facts and arguments pro and con adduced by the parties.”) (emphasis added). As the Supreme Court has explained, “[t]he determination of what may be useful to the defense can properly and effectively be made only by an advocate.” Dennis v. United States, 384 U.S. 855, 875, 86 S.Ct. 1840, 16 L.Ed.2d 973 (1966).

We should decline to raise non-jurisdictional defenses for another reason as well: fairness to the other party. Typically, it is not fair for courts to act as surrogate counsel for one side but not the other. See United States v. Pryce, 938 F.2d 1343, 1352 (D.C.Cir.1991) (Silberman, J., dissenting in part) (“We thus ordinarily have no right to consider issues not raised by a party in either briefing or argument ... because of the unfairness of such a practice to the other party.... ”); see infra, Part III.A.

Of course I acknowledge that there are exceptions to this rule of restraint. The Supreme Court has held that, in the interests of comity and federalism, courts may raise a habeas petitioner’s failure to exhaust state remedies sua sponte, even if the government does not. Granberry v. Greer, 481 U.S. 129, 131, 107 S.Ct. 1671, 95 L.Ed.2d 119 (1987); cf. Szuchon v. Lehman, 273 F.3d 299, 321 n. 13 (3d Cir.2001) (holding that in the interests of comity and federalism a court may raise procedural default sua sponte). And in Acosta v. Artuz, a case relied upon heavily by the Court in Long, the Second Circuit held that courts may raise non-jurisdictional defenses sua sponte where “the defenses implicate values beyond the interests of the parties.” Acosta, 221 F.3d at 121. The Acosta Court held that a district court may raise AEDPA’s statute of limitations sua sponte because it believed that defense fosters finality of convictions, promotes judicial efficiency and conservation of resources, and ensures the accuracy of judgments by resolving challenges to convictions while the record is fresh. Id. at 123. However, when a court examines a habeas petition for facial deficiencies pursuant to Rule 4, and finding none orders the government to answer, only to have the government fail to raise timeliness as a defense, each of those values become substantially less significant. When measured against the purpose and history of habeas corpus in our jurisprudence, those values shrink even further.

■ Initially, the Long Court noted that in considering the values beyond the interests of the parties served by AEDPA’s statute of limitations, comity and federalism are the “most important[ ].” Long, 393 F.3d at 403. The logic behind this statement renders it irrelevant. Unlike the defenses of exhaustion and procedural default, statutes of limitation do not implicate the interests of comity and federalism. Those defenses are designed to ensure that state courts have “an initial opportunity to pass upon and correct alleged violations of prisoners’ federal rights.” Duckworth v. Serrano, 454 U.S. 1, 3, 102 S.Ct. 18, 70 L.Ed.2d 1 (1981). The same cannot be said for a statute of limitations. When a state prisoner’s habeas petition is dismissed as untimely, the prisoner is not permitted to file his action in state court. Instead, he simply loses the ability to test the legality of his confinement. In the case of a section 2255 petition filed by a federal prisoner — as we have here — state courts are not involved in the trial and sentencing process whatsoever, and thus federalism and comity are simply irrelevant.

Similarly, judicial efficiency and economy are not implicated by a post-answer sua sponte dismissal pursuant to AEDPA’s statute of limitations. If a district court reviews a petition for deficiencies pursuant to Rule 4 and does not dismiss it, and the government then fails to raise the statute of limitations, the parties and the court begin to expend time and effort on the merits of the petition. At this point, judicial efficiency and economy are already lost. The very purpose of affirmative defenses, such as the statute of limitations, is to conserve judicial resources by requiring the parties to raise them early in the proceedings. Robinson, 313 F.3d at 134. Rescuing the government from its folly or inadvertence by permitting a district court to raise the statute of limitations after the parties have begun to address .the merits of the petition subverts that purpose, and may even have the opposite effect. If the statute of limitations is raised late in the proceedings, the parties must then brief yet an additional issue, which consumes the resources of all involved. I recognize that by permitting a district court to dismiss a habeas petition as untimely, some resources may be saved. But the same can be said for dismissing any lawsuit at any point. Yet it is not the general practice of this Court to raise the statute of limitations or other affirmative defenses either in civil or criminal cases in order to conserve judicial resources. Courts exist to resolve disputes. The resources of the courts should be used to that end. And what better use of judicial resources (or higher calling for the federal judiciary for that matter) could there be than ensuring that no one is incarcerated in violation of the law?

The majority makes a great deal of the interests of finality AEDPA was enacted to serve. There is no doubt that habeas corpus “presents a tension between the desire for finality, an end to the proceedings, and a desire to provide the chance for revisions, especially to correct errors.” Erwin Chemerinsky, Thinking About Habeas Corpus, 37 CASE W. RES. L. REV. 748, 789 (1987). As Professor Chemerin-sky has pointed out, “[tjhere obviously must be finality at some point; a time when the defendant has had sufficient opportunities for review and the chances of finding an error are too remote to justify further expenditure of resources.” Id. But on the other hand, conviction of the innocent or conviction in violation of the Constitution should not be tolerated. See id. Even those who have strongly emphasized a preference for curbing the scope of habe-as corpus have acknowledged that “conventional notions of finality” have diminished significance in the context of habeas. See Henry J. Friendly, Is Innocence Irrelevant? Collateral Attack on Criminal Judgments, 38 U. CHI. L. REV. 142, 150 (1970) (quotation omitted).

At the earliest, AEDPA’s statute of limitations begins to run when a prisoner’s conviction becomes final, upon the conclusion of direct review. See 28 U.S.C. §§ 2244, 2255. Indeed, it may well not begin for decades if, for instance, the petitioner relies on a retroactively applicable rule of constitutional law as recognized by the Supreme Court. 28 U.S.C. §§ 2244(d)(1)(C), 2255. Moreover, AED-PA’s statute of limitations is subject to equitable tolling. Fahy, 240 F.3d at 244. Many timely habeas petitions, therefore, might not be heard until years after conviction. In such a situation, the finality of the conviction is put in jeopardy — which, after all, is the very purpose of habeas review — as much as when a habeas petition is untimely filed and the government fails to raise a statute of limitations defense. Thus, concerns of finality are no more implicated after the government answers without raising timeliness than by many, if not most, habeas proceedings where timeliness is not an issue.

“In our adversary system, it is enough for judges to judge.” Dennis, 384 U.S. at 875, 86 S.Ct. 1840. Advocacy is best left to the parties. Thus, as a general rule, courts should not raise non-jurisdictional defenses on behalf of parties who do not raise the defenses for themselves. Acosta, 221 F.3d at 122. The Supreme Court has permitted departures from that general rule only when values beyond the interests of the parties are implicated. See Granberry, 481 U.S. at 131, 107 S.Ct. 1671; see also Szuchon, 273 F.3d at 321 n. 13. No such values are sufficiently implicated by a sua sponte dismissal for lack of timeliness where, as here, the government has failed to raise the statute of limitations in its answer.

III.

A.

Even if a sua sponte dismissal of the petitions in this case would serve values beyond the interests of the parties, I would still dissent because of the damage dismissal would work upon two countervailing values the majority fails to consider: the related notions of waiver and fundamental fairness.

The majority’s decision renders the concept of waiver a nullity. We held in Robinson, 313 F.3d at 134, that AEDPA’s statute of limitations is subject to waiver. In both Bendolph and Otero the government explicitly waived that defense. And while the majority reaffirms our holding in Robinson, at the same time it effectively destroys that portion of Robinson by holding that the government’s waiver is irrelevant. If a court may raise a non-jurisdictional defense once it has been waived, then waiver has no practical effect; it exists in theory alone. See Haskell v. Washington Township, 864 F.2d 1266, 1273 (6th Cir.1988) (explaining that if a district court may raise the statute of limitations sua sponte once it has been waived, “the waiver aspect of Rule 8(c) would have little meaning”). Thus, as a result of the majority opinion, it appears that AEDPA’s statute of limitations is no longer subject to waiver. I doubt very much whether courts will be so forgiving of a procedural error by a habeas petitioner.

As for the issue of fairness, Pliler v. Ford, 542 U.S. 225, 124 S.Ct. 2441, 159 L.Ed.2d 338 (2004), is instructive. In Pli-ler, the Supreme Court reversed a decision by the Ninth Circuit, which required district courts to give pro se habeas petitioners a warning that if they dismiss their petitions in order to first exhaust state remedies, AEDPA’s statute of limitations might bar them from refiling a future petition in federal court. According to the Ninth Circuit, the failure to provide the pro se habeas petitioner in that case with such a warning deprived him of the opportunity to make a “meaningful” choice concerning his petition. Id. at 2445 (citing Ford v. Hubbard, 330 F.3d 1086, 1102 (9th Cir.2003)). The Supreme Court disagreed. It held thát district courts need not warn pro se litigants that AEDPA’s statute of limitations might preclude them from filing any future petitions if they withdraw a timely petition. Id. at 2446. According to the Court, explaining habeas procedure and calculating the statute of limitations are tasks normally reserved for trained counsel, and “[Requiring district courts to advise a pro se litigant in such a manner would undermine the district judges’ role as impartial decisionmakers.” Id.

While one might argue that it is the pro se habeas petitioners — who are without the assistance of trained counsel — who need to be warned by district courts of AEDPA’s labyrinthine pitfalls most of all, the Court’s decision in Pliler is clear: district courts may not act as de facto counsel in habeas proceedings. Fairness dictates that we apply this rule equally to both sides, but the majority does not. The majority permits a district court to act as de facto counsel for the government, working together toward the common goal of dismissal of the petition. That is unfair. A habeas petitioner gets no help .from the courts, and the government needs none either. If, as Justice Thomas explained in Pliler, calculating the statute of limitations is a job ordinarily reserved for trained counsel, then that job should be left in the able hands of the government’s attorneys. Any other rule contravenes the fundamental notion that “the judiciary is on no side.... We judges must be strictly neutral with respect to all cases that come before us.” Pryce, 938 F.2d at 1352 (Silberman, J., dissenting in part).

The Court today permits and perpetuates a double standard. Cf. Latorre v. United States, 193 F.3d 1035, 1042 n. 3 (8th Cir.1999) (Lay, J., concurring in result only) (“It is ironic ... that in a § 2255 case a petitioner may not raise an issue on appeal when the issue has been procedurally defaulted in the district court, yet the court expressly ignores this principle when dealing with the United States government.”). It also sends a disturbing message: We will aid the government in a habeas proceeding, but not the petitioner. The mistakes of the government may be excused and ignored, but any error by the petitioner is fatal — perhaps figuratively, but too often literally. The favored-party status the majority affords to the government in habeas cases undermines both the appearance and fact of judicial neutrality, and I will have no part in it.

B.

Habeas corpus is not a luxury or an extravagance to be tolerated only when convenience permits. It is a fundamental protection of liberty “against arbitrary and wrongful imprisonment” that predates these United States. Chemerinsky, at 749. The Framers viewed it as “the highest safeguard of liberty,” Smith v. Bennett, 365 U.S. 708, 712, 81 S.Ct. 895, 6 L.Ed.2d 39 (1961) — a protection against arbitrary punishment and convictions to be “provided for in the most ample manner,” THE FEDERALIST NO. 83 (Alexander Hamilton). Since the 1970s, however, the road to habeas relief has “become a narrow! ], more tortuous track among concealed snake-pits and anti-personnel mines calculated to daze cartographers and daunt a modern Gilgamesh.” Anthony G. Amsterdam, Foreward to JAMES S. LIEBMAN & RANDY HERTZ, FEDERAL HABE-AS CORPUS PRACTICE AND PROCEDURE, at v (2d ed.1994). We continue to pile on “petty procedural barriers,” resulting in a “Byzantine morass of arbitrary, unnecessary, and unjustifiable impediments to the vindication of federal rights.” Coleman v. Thompson, 501 U.S. 722, 758-59, 111 S.Ct. 2546, 115 L.Ed.2d 640 (1991) (Blackmun, J., dissenting). This, in my view, is a great tragedy.

I constantly counsel myself and my-law clerks that somewhere in the mass of usually convoluted, often marginally-comprehensible pro se habeas petitions, there is another Clarence Earl Gideon, or one of the other faceless names for whom we do issue the Great Writ. Searching for those meritorious petitions is not only our duty, it is one of our most important. I am not alone in believing that the writ of habeas corpus may be the single most significant protection of individual rights in the Constitution. See Chemerinsky, at 749. I am simply adding my voice to the chorus. While technically the writ exists only as a procedural device, “its history is inextricably intertwined with the growth of fundamental rights of personal liberty.” Fay v. Noia, 372 U.S. 391, 399-400, 83 S.Ct. 822, 9 L.Ed.2d 837 (1963), abrogated on other grounds by Coleman, 501 U.S. at 722, 111 S.Ct. 2546. A threat to the writ’s vitality is a threat to those very fundamental rights. “It must never be forgotten that the writ of habeas corpus is the precious safeguard of personal liberty and there is no higher duty than to maintain it unimpaired.” Bowen v. Johnston, 306 U.S. 19, 26, 59 S.Ct. 442, 83 L.Ed. 455 (1939). In the name of reducing the docket of the district courts, and seduced by the lure of a one-line order, the majority evades its sacred duty. I dissent.

SLOVITER, Circuit Judge,

with whom Judges NYGAARD, MCKEE, AMBRO and FUENTES join, dissenting.

I join Judge Nygaard’s dissent but wish to note additionally that the opinion in Long v. Wilson, 393 F.3d 390 (3d Cir.2004), deviates from this court’s well-established rule that “a holding of a published opinion of the court may not be overruled without the approval of a majority of the en banc court.” Third Circuit IOP A(2). Although the opinion of the majority in this case refers to our decision in Robinson v. Johnson, 313 F.3d 128 (3d Cir.2002), without overruling it, the majority relies on our subsequent opinion in Long which, while also purporting to accept the Robinson holding, in fact eviscerates it. Notwithstanding the Commonwealth’s failure to timely raise the statute of limitations defense, Long allowed the Commonwealth to recoup that defense fourteen months later by its “endorse[ment] [of] the Magistrate Judge’s view that the habeas petition was untimely.” Long, 393 F.3d at 395. The Long court, by applying the stratagem of a constructive Rule 15(a) amendment, effectively nullified the Robinson requirement that the Commonwealth assert its statute of limitations defense in a timely manner.

The only effect of holding that the Government (or the Commonwealth in an appropriate case) waived its statute of limitations defense is that the matter will proceed on the merits. If the petitioner cannot show that his or her constitutional rights have been violated, the District Court will undoubtedly grant summary judgment for the Government in short order. If the petitioner has sufficient evidence of a violation of his or her rights, then the purpose of the habeas corpus statute will have been fulfilled.

Unlike the majority, I do not believe that “the public interest and the public reputation of judicial proceedings” will suffer if this court holds the Government to its waiver of the statute of limitations. Maj. Op. at 166. Indeed, it should only enhance its reputation by applying the procedural rules equally to petitioners and to the Government. 
      
      . Judge Van Antwerpen wrote the opinion of the Court in which Chief Judge Scirica and Judges Roth, Rendell, Barry, Smith and Fisher joined. Judge Nygaard filed an opinion concurring in part and dissenting in part, in which Judges Sloviter, McKee, Ambro, and Fuentes joined. Judge Sloviter filed an opinion dissenting, in which Judges Nygaard, McKee, Ambro, and Fuentes joined.
     
      
      . We acknowledge the consistently excellent advocacy provided by pro bono counsel on behalf of Messrs. Bendolph and Otero throughout the duration of these appeals, as well as the excellent briefs provided by both amici in advance of re-argument en banc.
      
     
      
      .Although the court may act upon what plainly appears from the motion, attached exhibits and record, not all limitations issues may appear in such manner. As such, notice and an opportunity to respond should be afforded during the Rule 4 stage. See footnote 15 infra.
      
     
      
      . The Supreme Court subsequently denied the petition for writ of certiorari on October 20, 1997.
     
      
      . Bendolph did not get the benefit of tolling for the time the petition was under consideration by the Supreme Court because the petition was untimely and therefore not properly filed. See, e.g., Merritt v. Blaine, 326 F.3d 157, 164 (3d Cir.2003) (" ‘an application is 'properly filed’ when its delivery and acceptance are in compliance with the applicable laws and rules governing filings,’ ” including " 'the time limits upon its delivery’ ”) (quoting Artuz v. Bennett, 531 U.S. 4, 8, 121 S.Ct. 361, 361, 148 L.Ed.2d 213 (2000)) (emphasis in Artuz ).
     
      
      . At the time this answer was filed, we had not yet rendered our decision in Kapral.
      
     
      
      . Although the District Court docket sheet and the parties cite August 24, 2000 as the date of the District Court’s order, our review of the record shows August 22, 2000 as the date of that order. The discrepancy does not affect the issues now before us.
     
      
      . The government initially conceded waiver in Bendolph, but now contends under Long, which we had not yet rendered at the time these cases were first argued, that waiver has not yet occurred.
     
      
      . The statute of limitations issue was first raised on August 19, 2003 when a panel of this Court entered an order granting Otero a certificate of appealability.
     
      
      . As in Bendolph, the government in Otero initially conceded waiver but has now reversed its position in light of our decision in Long.
      
     
      
      . See also 141 Cong. Rec. S7803-01 (daily ed. June 7, 1995) (statement of Sen. Nickles) ("[H]abeas procedures are wasteful. The current system is wasteful of limited resources. At a time when both State and Federal courts face staggering criminal caseloads, we can ill afford to make large commitments of judicial and prosecutorial resources to procedures of dubious value iri furthering the ends of justice.”); Williams, 529 U.S. at 436, 120 S.Ct. at 1490 (observing that, in passing the AED-PA, it was Congress’ "intent to avoid unneeded evidentiary hearings in federal habeas corpus”).
     
      
      . This conclusion is further reinforced, of course, by the purpose underlying Rule 4 of the Rules Governing Section 2254 and 2255 Cases, which promotes interests of judicial economy and efficiency.
     
      
      . Moreover, limitations periods should be construed consonant with the legislative scheme they support. See, e.g., American Pipe & Const. Co. v. Utah, 414 U.S. 538, 557-58, 94 S.Ct. 756, 768, 38 L.Ed.2d 713 (1974). As discussed throughout this opinion, Congress plainly intended strict reform of habeas corpus in passing the AEDPA, and the practical problems of attempting to re-litigate matters which are many years old are obvious.
     
      
      . In addition to the powers Granberry observed, courts may dismiss sua sponte for other reasons as well. See, e.g., Acosta, 221 F.3d at 121 (collecting cases); Kiser v. Johnson, 163 F.3d 326, 329 (5th Cir.1999) (collecting cases). Nor is the power limited to the habeas context. See, e.g., Gulf Oil Corp. v. Gilbert, 330 U.S. 501, 502, 67 S.Ct. 839, 840, 91 L.Ed. 1055 (1947) (inherent power to dismiss pursuant to the doctrine of forum non conveniens); Molinaro v. New Jersey, 396 U.S. 365, 366, 90 S.Ct. 498, 499, 24 L.Ed.2d 586 (1970) (inherent power to dismiss if the defendant is a fugitive).
      Analogously instructive is the Supreme Court's decision in Link v. Wabash R. Co., 370 U.S. 626, 82 S.Ct. 1386, 8 L.Ed.2d 734 (1962). Link rejected the argument that the power afforded to civil defendants under Fed. R.Civ.P. 41 to move for involuntary dismissals necessarily extinguishes, by negative implication, the courts’ powers to dismiss sua sponte. Link, 370 U.S. at 629-30, 82 S.Ct. at 1388 (observing courts have inherent power to dismiss sua sponte "to clear their calendar of cases ... dormant because of inaction or dila-toriness ....”). Link counsels that concerns arising from sua sponte dismissals are best addressed not by curtailing inherent powers, but rather by determining whether a court has acted "within the permissible range of the court's discretion.” Id. at 633, 82 S.Ct. at 1389. We did as much in Long, an approach we reaffirm today.
     
      
      
        . Thus it cannot be doubted that, at the very least, courts possess a sua sponte power during those stages of a habeas case governed by Rule 4 of the Rules Governing Section 2254 and Section 2255 Cases. That rule states in pertinent part:
      If it plainly appears from the motion, any attached exhibits, and the record of prior proceedings that the moving party is not entitled to relief, the judge must dismiss the motion and direct the clerk to notify the moving party.
      
        See § 2255 Rule 4(b); see also § 2254 Rule 4. As this language anticipates, the issues relevant to timeliness may not all appear on the face of a motion or petition, and for this reason courts should give notice that a limitations problem may exist, as well as provide an opportunity for a habeas movant or petitioner to respond. See, e.g., Hill v. Braxton, 277 F.3d 701, 707 (4th Cir.2002); Acosta v. Artuz, 221 F.3d 117, 121 (2d Cir.2000). We make no distinction as between habeas movants filing pro se and those represented by counsel. See, e.g., McMillan v. Jarvis, 332 F.3d 244, 245 (4th Cir.2003) (holding Hill's notification requirement applies to habeas movants represented by counsel as well as those proceeding pro se).
      
     
      
      . For this reason, federal habeas courts acting sua sponte need not invite the government to amend an answer pursuant to Rule 15(a), nor wait to see if the government responds. See also Carlisle v. United States, 517 U.S. 416, 437, 116 S.Ct. 1460, 1471, 134 L.Ed.2d 613 (1996) (Stevens, J., dissenting) ("It is quite wrong ... to assume that a judge is nothing more than a referee whose authority is limited to granting or denying motions advanced by the parties."). And while government prosecutors have both prosecutorial discretion and heightened ethical duties to do justice, such considerations do not justify subordinating judicial power to the presence or absence of the AEDPA limitations defense in a government answer or motion.
     
      
      . If nothing else, if the power exists, there is nothing to suggest that Congress has taken it away. While Congress may limit the courts' inherent powers, we should not "lightly assume that Congress intended to do so." Chambers v. NASCO, Inc., 501 U.S. 32, 47, 111 S.Ct 2123, 2134, 115 L.Ed.2d 27 (1991) (internal quotation omitted). Here, the statutory language and legislative history are silent, and "something far more than ambiguous silence is required to withdraw a district court's inherent power.” Carlisle, 517 U.S. at 449, 116 S.Ct. at 1477 (Stevens, J., dissenting).
     
      
      . Although we have not yet had occasion to reach the question, other courts of appeals have held the AEDPA statute of limitations constitutional in the face of per se challenges brought under the Suspension Clause of the United States Constitution, Art. I, § 9, cl. 2. See, e.g., Wyzykowski v. Dep’t of Corr., 226 F.3d 1213, 1217 and n. 3 (collecting cases). Cf. Felker v. Turpin, 518 U.S. 651, 664, 116 S.Ct. 2333, 135 L.Ed.2d 827 (1996) (AEDPA's restrictions on successive petitions "do not amount to a ‘suspension’ of the writ”); Swain v. Pressley, 430 U.S. 372, 381, 97 S.Ct. 1224, 51 L.Ed.2d 411 (1977) (holding that the Suspension Clause is violated only where habeas corpus is rendered "inadequate or ineffective”).
     
      
      . For these reasons, as a matter of elapsed time, the first practicable chance to knowledgeably raise a timeliness issue often arises later in the life of a habeas case than it would in an ordinary civil one. Thus we have already recognized the need for a longer pre-waiver period in habeas. See Robinson, 313 F.3d at 136-37 (allowing post-answer raising of the defense at the "earliest practicable moment”). Long, consistent with Robinson, then confirmed that prejudice is the "ultimate issue.” See Long, 393 F.3d at 401. Our earliest practicable moment standard in Robinson and our prejudice standard in Long correctly balance the realities summarized in Pliler, 124 S.Ct. at 2446, and a habeas petitioner's due process rights.
     
      
      . We do not reach the issue of whether the government's actions constituted an inadvertent waiver, intentional waiver, or no waiver because, no matter the answer to that question, the court possessed the ability to act sua sponte.
      
     
      
      . At the time, we had not yet rendered our decision in Kapral, supra, and in any event the petition for certiorari had been improperly altered.
     
      
      . Although the issue has not been raised before us, it appears that the delay in Otero may exceed that in Bendolph and Long, as Otero filed his § 2255 motion on June 25, 2001. As noted, delay alone is not dispositive and must be considered along with the other components of prejudice that we identified in Long and reaffirm today.
     
      
      .We leave for another day whether or not a district court may apply the statute of limitations if the government has intentionally waived this defense and continues to do so after the district court has raised the issue.
     
      
      . Although Rule 5(b) of the Section 2255 Rules does not require the government to state whether any statute of limitations applies, as the majority points out, "we have followed the practice, whenever we decide an AEDPA issue that arises under § 2254 and the same holding would analytically be required in a case arising under § 2255, or vice versa, of so informing the district courts.” Miller, 145 F.3d at 619 n. 1. I agree with the majority that on the question of a district court's continuing authority (or lack thereof) to raise the statute of limitations sua sponte after the government's answer, we should treat section 2254 and section 2255 cases the same. I reach a different conclusion as to that question, of course.
     
      
      . The Federal Rules of Civil Procedure may be made applicable to habeas cases "to the extent they are not inconsistent with any statutory provisions or [the Habeas] rules.” Section 2254 Rule 11; see Section 2255 Rule 12. Applying Civil Procedure Rule 8(c), which mandates that parties set forth any affirmative defenses they might have — including the statute of limitations — in a responsive pleading, is consistent with the mandate of Rule 5(b) of the Section 2254 Rules that the government shall state in its answer whether the petition is barred by a statute of limitations.
     
      
      . In United States v. Otero, 02-2624, counsel for the United States stated during oral argument before the panel: “We waived the statute of limitations. There’s no question under this Court's Robinson decision that we waived the statute of limitations.” (Oral Argument Tr. at 36). Similarly, in United States v. Bendolph, 01-2468, counsel for the United States explained, "we waived the statute of limitations.” (Oral Argument Tr. at 56).
     
      
      . Incidentally, had Congress wanted to protect AEDPA’s statute of limitations from waiver, it could have done so by statute as it. did for the defense of failure to exhaust state remedies. Pursuant to 28 U.S.C. § 2254(b)(3), "[a] State shall not be deemed to have waived the exhaustion requirement ... unless the State, through counsel, expressly waives the requirement.” Congress has afforded the defense of AEDPA's statute of limitations no such protection, and even if it had, counsel for the United States explicitly waived the defense in each of these consolidated cases. The majority simply excuses that waiver, instead vesting in the district courts the discretion whether to raise the statute of limitations sua sponte in any given case. That grant of authority is likely to create vast disparities concerning the treatment of government waiver between judges and from one case to the next. Those disparities will in turn be visited upon petitioners.
     
      
      .Indeed, courts routinely dismiss petitions, standing upon mere punctilios in the law.
     
      
      . I do not believe my colleagues in the majority intend to be less principled or less fair than I. I do believe, however, that the majority sacrifices a little of both principle and fairness at the altar of expedience. Courts have admittedly crowded dockets. Those dockets include many habeas petitions, and I fear that the petitions with merit are outnumbered by those without. Any rale that would permit district courts to more easily dispose of habeas petitions might therefore seem desirable. But when individual liberty is at stake — as is the case with any habeas petition — expedience and self-interest ought not inform our decisions.
     