by Douglas Ankney

The United States Court of Appeals for the First Circuit affirmed the U.S. District Court for the District of Puerto Rico’s grant of 28 U.S.C. § 2254 habeas relief, holding that the Commonwealth intelligently waived any § 2244(d)(1)(C) timeliness defense by knowingly omitting it from their answer despite awareness of its availability. Furthermore, the Court held that the District Court abused its discretion in raising and resolving the waived defense sua sponte, rendering equitable tolling moot and leaving no basis to disturb the judgment.

Background

On July 24, 2001, David Núñez-­Pérez (“Núñez”) was indicted in the District Court on one count of federal carjacking, 18 U.S.C. § 2119(3), and three related federal firearms counts, 18 U.S.C. § 924(c)(1)(A)(ii); 18 U.S.C. § 922(g)(1); 18 U.S.C. § 924(a)(2). Many months later, in February 2002, Núñez was indicted in Puerto Rico superior court under Puerto Rico law on charges arising from the same alleged incident, specifically carjacking, first-­degree murder, and two weapons possession counts.

On May 2, 2002, Núñez pleaded guilty in federal court to the carjacking charge and was soon thereafter sentenced to 10 years’ imprisonment. The federal firearms charges were dismissed. Then, on November 14, 2003, a jury in Puerto Rico superior court found Núñez guilty of the carjacking and weapons charges under Puerto Rico law, as well as the lesser-­included offense of manslaughter under Puerto Rico law. The superior court imposed a 69-­year prison sentence for these convictions, to be served consecutively to his 10-­year federal sentence.

Núñez timely appealed his Puerto Rico convictions on various grounds, including a double jeopardy challenge asserting that he was already serving a federal sentence for the same conduct. The Puerto Rico Court of Appeals rejected the double jeopardy claim, holding that because Puerto Rico and the federal government are separate sovereigns, “conduct that constitutes a crime in both jurisdictions may be punished independently by both entities[] without violating the constitutional clause against double jeopardy or constituting multiple punishments for the same conduct.” Núñez petitioned for certiorari to the Puerto Rico Supreme Court, which denied the petition on February 2, 2007, rendering his convictions final.

Nearly a decade later, on June 9, 2016, the U.S. Supreme Court held in Puerto Rico v. Sánchez Valle, 579 U.S. 59 (2016), that, because the United States and Puerto Rico are not separate sovereigns for purposes of the Double Jeopardy Clause, neither may “successively prosecute a single defendant for the same criminal conduct.”

On June 20, 2017 – 373 days after Sánchez Valle was issued and one year and 11 days after that decision – Núñez filed a Rule 192.1 postconviction collateral relief motion (“Rule 192.1 Motion”) in Puerto Rico superior court. The motion argued that the rule announced in Sánchez Valle barred his Puerto Rico carjacking and manslaughter convictions. The superior court denied the motion on September 12, 2018. Núñez’s petitions for certiorari to the Puerto Rico Court of Appeals and Puerto Rico Supreme Court were denied, respectively, on December 18, 2018, and February 15, 2019. The Puerto Rico Supreme Court also denied Núñez’s two motions for reconsideration.

Acting pro se, Núñez filed a 28 U.S.C. § 2254 habeas corpus petition on May 21, 2019, in the U.S. District Court for the District of Puerto Rico against several respondents, including the Secretary of the Puerto Rico Department of Corrections and Rehabilitation (collectively, “Respondents”). The petition contended that the rule in Sánchez Valle was retroactively applicable to his Puerto Rico carjacking and manslaughter convictions, entitling him to relief under the Double Jeopardy Clause. Counsel later appeared on his behalf and, on October 23, 2020, filed a supplemental motion in support.

On February 23, 2021, Núñez moved for an order directing Respondents to answer the petition, which the District Court granted. Respondents filed a motion to dismiss on March 29, 2021, arguing the petition was time-­barred under the one-­year statute of limitations in 28 U.S.C. § 2244(d)(1). Invoking § 2244(d)(1)(A), Respondents argued the limitations period began when Núñez’s convictions became final on February 2, 2007, and thus expired on February 2, 2008. They emphasized that § 2244(d)(1)(C) – which restarts the period from “the date on which [a newly recognized constitutional right was] initially recognized by the Supreme Court” if “made retroactively applicable to cases on collateral review” – did not apply because Sánchez Valle was not expressly declared retroactive. Santana-­Ríos v. United States, 235 F. Supp. 3d 386 (D.P.R. 2017). Respondents further argued that §§ 2244(d)(1)(B) and (D) were inapplicable.

On June 3, 2021, the District Court ordered supplemental briefing on whether Sánchez Valle established a right that was “(1) ‘newly recognized by the Supreme Court,’ and (2) ‘made retroactively applicable to cases on collateral review’” under § 2244(d)(1)(C). In responsive filings, Núñez asserted that it did; Respondents reiterated untimeliness under § 2244(d)(1)(A) and contended Sánchez Valle did not trigger § 2244(d)(1)(C).

On November 4, 2021, the District Court held a hearing on the motion to dismiss. Respondents asserted for the first time that the petition was time-­barred “[n]ot only … taking [as] a start date the date that the petitioner’s conviction and sentence became final, but … also tak[ing] the date that the petitioner filed [his] Rule 192.1 Motion” and “calculat[ing] from the date that the [Sánchez Valle] decision was published,” without further elaboration on why the petition itself would be untimely under that framework.

The District Court then ordered Respondents to answer the petition pursuant to Rule 5 of the Rules Governing § 2254 Cases, which requires stating whether any claim is barred by the statute of limitations. In their answer on February 4, 2022, Respondents reprised their § 2244(d)(1)(A) untimeliness argument as their affirmative defense. Although they noted in response to the petition that the Rule 192.1 Motion was filed “373 days after” Sánchez Valle, they did not assert untimeliness under § 2244(d)(1)(C) as an affirmative defense. Instead, they acknowledged § 2244(d)(1)(C) “in the alternative” but argued only that Sánchez Valle did not qualify to trigger it.

On March 31, 2022, the District Court sua sponte raised the possibility that the petition was untimely under § 2244(d)(1)(C) because the Rule 192.1 Motion – filed before the § 2254 petition – had been submitted 11 days after the one-­year period from Sánchez Valle expired, noting neither party had addressed whether that period expired before the Rule 192.1 Motion. The District Court ordered a joint memorandum addressing § 2244(d)(1)(C) untimeliness and whether Respondents would waive any limitations defense.

In the joint memorandum, Núñez acknowledged the Rule 192.1 Motion was filed 11 days after § 2244(d)(1)(C)’s period would otherwise have expired but contended he was entitled to equitable tolling under Holland v. Florida, 560 U.S. 631 (2010), because he had been “actively pursuing his constitutional rights of double jeopardy” and the limitations period “does not set forth an inflexible rule requiring dismissal whenever the one-­year clock has run.” Respondents countered that § 2244(d)(1)(C) expired before the Rule 192.1 Motion, Núñez had not previously alleged equitable tolling, and they would not waive the statute of limitations under any § 2244(d)(1) provision.

On August 1, 2022, the District Court denied Respondents’ motion to dismiss and granted the petition. It ruled that § 2244(d)(1)(C) governed because Sánchez Valle announced a new retroactively applicable rule; that Núñez satisfied Holland’s diligence and extraordinary-­circumstances prongs for equitable tolling of the 11-­day delay on the “limited record” and given the “disproportionate” stakes of a “life sentence” under a “case-­by-­case” equitable approach; and that, on the merits, the Puerto Rico courts’ rejection of the Rule 192.1 Motion was “contrary to, or involved an unreasonable application of, clearly established [f]ederal law,” i.e., § 2254(d)(1), because it “failed to apply the Supreme Court’s federal retroactivity analysis.” Because Respondents admitted Núñez’s Puerto Rico carjacking and manslaughter convictions were identical to his federal carjacking conviction, the District Court ruled the Puerto Rico convictions were barred by the Double Jeopardy Clause and granted habeas relief.

Respondents moved for reconsideration, which the District Court denied, and timely filed a notice of appeal, challenging only the District Court’s equitable tolling ruling under § 2244(d)(1)(C).

Analysis

The First Circuit affirmed the District Court’s grant of habeas relief, holding that the Respondents waived any argument that Núñez’s § 2254 petition was untimely under § 2244(d)(1)(C) by knowingly failing to assert that ground in their answer. As a result, the District Court abused its discretion in raising and addressing the § 2244(d)(1)(C) defense sua sponte after the Respondents had relinquished it. See Day v. McDonough, 547 U.S. 198 (2006); Wood v. Milyard, 566 U.S. 463 (2012). Additionally, because the District Court’s equitable tolling adjudication “both followed from and depends on the waived § 2244(d)(1)(C) defense,” the Court declined to address whether the District Court erred in applying equitable tolling. With no independent basis presented on appeal to overturn the grant of relief, the judgment was affirmed.

Waiver vs. Forfeiture in Habeas Limitations Defenses

“Ordinarily in civil litigation, a statutory time limitation is forfeited if not raised in a defendant’s answer or in an amendment thereto.” Day; see also Fed. R. Civ. P. 8(c); Habeas Rule 5(b). The Court noted that based on “the principle of party presentation [that is] basic to our adversary system,” courts generally may not raise an affirmative defense, such as statute of limitations, that a party has not itself asserted. Wood v. Milyard, 566 U.S. 463 (2012).

In the habeas context, however, a “modest exception” permits District Courts to “consider a forfeited habeas defense when extraordinary circumstances so warrant,” such as when the Government’s failure to assert the defense is “inadvertent.” Wood (citing Day). Forfeiture occurs through neglect or oversight, preserving judicial authority to resurrect the defense, the Court explained.

In contrast, “should a State intelligently choose to waive a statute of limitations defense, a District Court would not be at liberty to disregard that choice.” Day; see Wood (federal courts may “resurrect” only forfeited defenses). Waiver is the “intentional relinquishment or abandonment of a known right.” Wood (quoting Kontrick v. Ryan, 540 U.S. 443 (2004)). A District Court has no “discretion to take up [a] timeliness [defense]” sua sponte when the Government “is aware of [the] limitations defense and intelligently chooses not to rely on it,” or when the defense is “strategically” withheld, the Court stated. Wood (quoting Day).

The Court explained that in Day, the State asserted in its responsive pleading that the petition was “filed after 352 days of untolled time” and thus “timely” – a concession based on an “evident miscalculation.” The District Court detected the “obvious computation error,” raised timeliness sua sponte, and dismissed. Id. The Supreme Court affirmed, concluding that confronted with a “plain” and “inadvertent error,” the District Court did not abuse its discretion. Id. Notably, the Day Court emphasized that an “intelligent” waiver would bind the court.

In Wood, the State “twice informed the District Court that it ‘[would] not challenge, but [was] not conceding’ the timeliness” of the petition. In a pre-­answer motion, the State noted the petition was “arguabl[y]” untimely but expressly opted to rely on other defenses. The Tenth Circuit later dismissed sua sponte as untimely on appeal. The Supreme Court reversed, ruling the appellate court abused its discretion by overlooking waiver. The State’s conduct constituted waiver because it did not stem from “inadvertent error” but reflected an “express[] … clear and accurate understanding of the timeliness issue” while choosing “in no uncertain terms, to refrain from interposing” the defense. Id.

Application: Intelligent Waiver
of § 2244(d)(1)(C) Defense

Turning to the present case, the Court observed that Respondents failed to argue in their answer – or in their motion to dismiss or any pre-­answer filing – that the petition was untimely under § 2244(d)(1)(C). Their sole limitations defense was untimeliness under § 2244(d)(1)(A), based on Sánchez Valle not triggering § 2244(d)(1)(C) due to lack of retroactivity.

The Court stated that no basis exists to treat this omission as inadvertent. Respondents specified in their answer the exact filing date of Núñez’s Rule 192.1 Motion and that it “post-­dated Sánchez Valle by more than 365 days.” They discussed § 2244(d)(1)(C) when advancing their § 2244(d)(1)(A) argument, demonstrating awareness of its potential relevance. Yet, in putting forth affirmative defenses, they opposed the petition only on the ground that Sánchez Valle “does not state a retroactively applicable rule” and § 2244(d)(1)(C) therefore does not apply, the Court observed. Although Respondents stated at the motion-­to-­dismiss hearing that the petition was untimely “calculat[ing] from the date that the [Sánchez Valle] decision was published,” they “failed to explain it” and “never pressed it” in any filing – not the preceding motion to dismiss nor the subsequent answer.

Consequently, Respondents “knew [they] had an ‘arguable’ statute of limitations defense” under § 2244(d)(1)(C) yet chose not to raise it. Wood, 566 U.S. at 474. By limiting their answer to a § 2244(d)(1)(A) defense tied to non-­retroactivity, they intentionally steered the District Court away from the question of timeliness under § 2244(d)(1)(C) and towards the question of Sánchez Valle’s retroactivity, according to the Court.

The District Court later raised § 2244(d)(1)(C) untimeliness sua sponte. Respondents then asserted in the joint memorandum that they would not waive the statute of limitations – but only after having “knowingly … relinquish[ed]” the § 2244(d)(1)(C) defense through their answer, the Court stated. Even in the joint memorandum, they “continued to treat the issue as merely implicating the retroactivity of Sánchez Valle,” arguing retroactive application “would overturn almost 30 years’ worth of convictions” and “undermine the principle of finality.” The Court noted that only on appeal did they pivot to defend untimeliness squarely under § 2244(d)(1)(C).

Conclusion

Thus, the Court held that Respondents “intelligently” waived their § 2244(d)(1)(C) limitations defense by knowingly failing to assert it in their answer. It further held that to the extent the District Court disregarded that waiver by raising and addressing the defense sua sponte, it abused its discretion.

Accordingly, the Court affirmed the District Court’s judgment granting the habeas petition. See: Núñez-­Pérez v. Escobar-­Pabón, 133 F.4th 33 (1st Cir. 2025).  

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