with whom KOZINSKI, Circuit Judge, joins, Specially Concurring.
I agree with the majority that the AED-PA’s statute of limitations never should have been applied to Kelly because, under the analysis of Hohn v. United States, —- U.S. -, 118 S.Ct. 1969, 141 L.Ed.2d 242 (1998), his habeas case was pending prior to the enactment of the AEDPA.
However, I write separately to express my disagreement with the majority’s unnecessary and wholesale rejection of res judicata in the habeas context. Both Congress and the Supreme Court have made it clear that in the absence of unusual circumstances, habeas petitioners cannot continue to litigate issues that have been or could have been litigated already in habeas proceedings. When Congress amended § 2244 of the habeas corpus statute in 1966, it specifically stated that “the purpose of these new subsections is to add to section 2244 of title 28, United States Code, provisions for a qualified application of the doctrine of res judicata.” S.Rep. No. 89-1797, at 2 (1966) (emphasis added). The Supreme Court has agreed. See Calderon v. Thompson, 523 U.S. 538, 118 S.Ct. 1489, 1500-1501, 140 L.Ed.2d 728 (1998). See also Schlup v. Delo, 513 U.S. 298, 318-19, 115 S.Ct. 851, 130 L.Ed.2d 808 (1995) (successive petition standard is a “qualified application of res judicata”); Felker v. Turpin, 518 U.S. 651, 116 S.Ct. 2333, 2340, 135 L.Ed.2d 827 (1996) (“the new restrictions on successive petitions constitute a modified res judicata rule, a restraint on what is called in habeas corpus practice ‘abuse of the writ’ ”); *543McCleskey v. Zant, 499 U.S. 467, 486, 111 S.Ct. 1454, 113 L.Ed.2d 517 (1991) ( “subpar-agraph (b) [to 28 U.S.C. § 2244] establishes a qualified application of res judicata”).
By definition, a petition for writ of habeas corpus is a collateral attack on a final judgment. It is in that sense that res judicata does not apply to habeas corpus proceedings. That is a far cry from a rule of res judicata that prevents a habeas petitioner who has already litigated X in habeas proceeding from relitigating X in new habeas proceedings without good excuse. This case illustrates the problem. In 1992, Kelly started his first habeas proceeding by requesting the appointment of counsel. In 1997, after the AEDPA statute of limitations had run, the state moved to dismiss the proceedings on the grounds that no petition for writ of habe-as corpus had ever been filed and that the time to file had run out. Kelly responded to the motion to dismiss with two arguments: First, that the AEDPA’s statute of limitations did not apply to him; and second, that even if it did, the statute of limitations was equitably tolled by his incompetency. At no time did Kelly also claim equitable tolling based on his reliance on Judge Hatter’s order. In fact, when this case was argued to the Kelly III panel, this revealing colloquy occurred:
Judge Tashima: Suppose, suppose, we don’t agree that this is a pending case. In other words, that the AEDPA does apply to this case. Your position then is what?
Mr. Neuhoff,
Kelly’s counsel: Well, at that point, this Court is entitled to ... if there is any ground appearing in the record from which the district court’s decision and its exercise of discretion can be upheld then the court can deny the writ [of mandamus sought by the state] on that basis and another ground here is equitable tolling.
Judge Tashima: What appears in the record to support that?
Mr. Neuhoff: What appears in the record is that the district court has before it prima facie evidence, at least, that Mr. Kelly is: (a) incompetent to proceed and assist counsel in his habeas proceedings and (b) is incompetent to be executed.
* * * 1
Conspicuously absent was anything from Kelly’s counsel along the lines of “... and (c) Kelly or his lawyers relied in good faith on Judge Hatter’s order.” Judge Hatter’s order, which looms so large now, wasn’t even mentioned.
The upshot of that oral argument was the decision in Kelly III holding that Kelly’s incompetency did not constitute grounds for equitable tolling. After Kelly III was decided, the state again moved the district court to dismiss Kelly’s habeas proceedings as time-barred. This time, for the first time, Kelly raised Judge Hatter’s order as a basis for equitable tolling.
One can only wonder how many additional theories of equitable tolling Kelly had in reserve. One must also wonder how this court could possibly permit him to litigate one of his grounds for equitable tolling and then, after he loses, to raise additional grounds for equitable tolling of which he was previously aware. The record in this case is devoid of any explanation of why Kelly’s counsel did not raise the currently proffered ground for equitable tolling earlier, either in response to the state’s motion to dismiss in the district court or in connection with the petition for writ of mandamus in this court in Kelly III. As a result, in my view, he is barred from belatedly raising it now unless his default is excused by a showing of cause and prejudice or manifest injustice.
The problem raised by the Supreme Court’s decision in Hohn is a different matter. “[A] court should not reopen issues decided in earlier stages of the same litigation. The doctrine does not apply if the court is convinced that [its prior decision] is clearly erroneous and would work a manifest injustice.” Agostini v. Felton, 521 U.S. 203, 117 S.Ct. 1997, 138 L.Ed.2d 391 (1997) (citations and internal quotation marks omitted). *544The Supreme Court’s decision in Hohn, handed down after both Kelly III and Kelly IV were decided, demonstrates that Kelly-should not have been deemed barred from filing his petition for writ of habeas corpus by the AEDPA statute of limitations in the first place. It would be unjust to persist in that error.
. Transcript of argument of Calderon v. U.S.D.C. (Kelly), (“Kelly III"), September 5, 1997 at 13.