Perhaps the most important jurisprudential aspect of Alleyne concerns a dueling battle between Alito and Sotomayor on stare decisis.

Justice Alito takes the Court in Alleyne to task for overturning Harris without due concern for stare decisis. If Harris can be overturned, why not Apprendi.

The Court overrules a well-entrenched precedent with barely a mention of stare decisis. See ante, at 16, n. 6. Stare decisis is, of course, not an “inexorable command” in the field of constitutional law. Payne v. Tennessee, 501 U. S. 808, 828 (1991). Nevertheless, the Court ought to be consistent in its willingness to reconsider precedentIf Harris v. United States, 536 U. S. 545 (2002), and McMillan v. Pennsylvania, 477 U. S. 79 (1986), can be cast aside simply because a majority of this Court now disagrees with them, that same approach may properly be followed in future cases. See Arizona v. Gant, 556 U. S. 332, 358– 364 (2009) (ALITO, J., dissenting).

… The Court’s decision creates a precedent about precedent that may have greater precedential effect than the dubious decisions on which it relies

Notably, the Chief’s dissenting opinion, joined by Scalia and Kennedy does not take exception with the application of stare decisis.

I will not quibble with the majority’s application of our stare decisis precedents. But because I believe the major- ity’s new rule—safeguarding the power of judges, not juries—finds no support in the history or purpose of the Sixth Amendment, I respectfully dissent.

Of course, the Chief famously wrote separately about stare decisis in Citizens United.

At the very end of Justice Alito’s dissenting opinion he adds a three-page long footnote (that includes the elusive blank page!) faulting the majority for overturning Harris v. United States, and in particular taking exception with the concurring opinion by Justice Sotomayor. This lengthy footnote looks like it was added on late in the game, after reading Soto’s concurrence.

Speaking for herself, JUSTICE GINSBURG, and JUSTICE KAGAN—but not for the Court—JUSTICE SOTOMAYOR argues that Harris’ stare decisis value is undermined by the subsequent reasoning of the Court’s Apprendi line of cases and by the fact that no one rationale in Harris commanded five votes. I disagree.

Justice Sotomayor wrote separately, likely in response to Alito’s opinion, to explain when it is appropriate to reverse precedent, and address Justice Alito’s charges.

Of course, under our doctrine of stare decisis, establishing that a decision was wrong does not, without more, justify overruling it. While stare decisis is not an “inexorable command,” Hohn v. United States, 524 U. S. 236, 251 (1998) (internal quotation marks omitted), it is “a basic self-governing principle within the Judicial Branch, which is entrusted with the sensitive and difficult task of fashioning and preserving a jurisprudential system that is not based upon ‘an arbitrary discretion,’” Patterson v. McLean Credit Union, 491 U. S. 164, 172 (1989) (quoting The Federalist, No. 78, p. 490 (H. Lodge ed. 1888) (A. Hamilton)). We generally adhere to our prior decisions, even if we question their soundness, because doing so “promotes the evenhanded, predictable, and consistent development of legal principles, fosters reliance on judicial decisions, and contributes to the actual and perceived integrity of the judicial process.” Payne v. Tennessee, 501 U. S. 808, 827 (1991). To protect these important values, we require a “‘“special justification”’” when departing from precedent. Dickerson v. United States, 530 U. S. 428, 443 (2000). A special justification is present here.

Sotomayor identifies several justifications. First, that this case concerns a procedural rule:

As an initial matter, when procedural rules are at issue that do not govern primary conduct and do not implicate the reliance interests of private parties, the force of stare decisis is reduced. See United States v. Gaudin, 515 U. S. 506, 521 (1995); Payne, 501 U. S., at 828. And any reliance interest that the Federal Government and state governments might have is particularly minimal here because prosecutors are perfectly able to “charge facts upon which a mandatory minimum sentence is based in the indictment and prove them to a jury.”

Second, Sotomayor observes the case has been eroded by subsequent precedents:

In this context, stare decisis does not compel adherence to a decision whose “underpinnings” have been “eroded” by subsequent developments of constitutional law. Gaudin, 515 U. S., at 521. In rejecting a constitutional challenge to a state statute that increased a defendant’s minimum sentence based on judicial factfinding, McMillan relied on a distinction between “elements” and “sentencing factors.” 477 U. S., at 86. That distinction was undermined by Apprendi, where we held that a legislature may not “remove from the jury the assessment of facts that increase the prescribed range of penalties to which a criminal defendant is exposed.”

Alito is not persuaded.

In my view, Harris’ force is not vitiated by the Court’s Apprendi line of cases, for two reasons. First, that line of cases is predicated on a purported Sixth Amendment requirement that juries find facts that increase maximum penalties, not mandatory minimums. Accordingly, as THE CHIEF JUSTICE’s dissent persuasively explains, ante, at 1–7, Apprendi and its progeny have no impact on the distinct question resolved by Harris, which does not bear on the jury right. Second, the Apprendi line is now too intellectually incoherent to undermine any “contrary” precedents. If the rationale of Apprendi—which, as broadly construed by the Court in this case, is that “[a]ny fact that, by law, increases the penalty for a crime is an ‘element’ that must be submitted to the jury and found beyond a reasonable doubt,” ante, at 1—were taken seriously, discretionary sentencing, as prescribed by 18 U. S. C. §3553(a), should also be held to violate the Sixth Amendment. But a majority of the Court has not been willing to go where its reasoning leads

Third, Sotomayor remarked that members of the Court have continued to question the precedent–such as Breyer’s perpetual dissent of Apprendi.

We have said that a decision may be “of questionable precedential value” when “a majority of the Court expressly disagreed with the rationale of [a] plurality.” Seminole Tribe of Fla. v. Florida, 517 U. S. 44, 66 (1996). And Harris has stood on especially weak ground because its vitality depended upon the possibility that the Court might retreat from Apprendi. See Harris, 536 U. S., at 569–570 (opinion of BREYER, J.). That has not happened. Instead, while individual Members of this Court have continued to question Apprendi, see post, at 1–2 (opinion of BREYER, J.); post, at 1–2 (ALITO, J., dissenting), its rule has become even more firmly rooted in the Court’s Sixth Amendment jurisprudence in the decade since Harris.

Update: In Arizona v. Inter Tribal Council of Ariz., Inc., Justice Scalia makes a similar point about the precedential value of plurality opinions, curiously also citing Seminole Tribe. H/T Greg

In Mitchell, the judgment of the Court was that Congress could compel the States to permit 18-year-olds to vote in federal elections. Of the five Justices who concurred in that outcome, only Justice Black was of the view that congressional power to prescribe this age qualification derived from the Elections Clause, 400 U. S., at 119–125, while four Justices relied on the Fourteenth Amendment, id., at 144 (opinion of Douglas, J.), 231 (joint opinion of Brennan, White, and Marshall, JJ.). That result, which lacked a majority rationale, is of minimal precedential value here. See Seminole Tribe of Fla. v. Florida, 517 U. S. 44, 66 (1996); Nichols v. United States, 511 U. S. 738, 746 (1994); H. Black, Handbook on the Law of Judicial Precedents 135–136 (1912). Five Justices took the position that the Elections Clause did not confer upon Congress the power to regulate voter qualifications in federal elections. Mitchell, supra, at 143 (opinion of Douglas, J.), 210 (opinion of Harlan, J.), 288 (opinion of Stewart, J., joined by Burger, C. J., and Blackmun, J.). (Justices Brennan, White, and Marshall did not address the Elections Clause.) This last view, which commanded a majority in Mitchell, underlies our analysis here. See also U. S. Term Limits, 514 U. S., at 833. Five Justices also agreed that the Fourteenth Amendment did not empower Congress to impose the 18-year-old-voting mandate. See Mitchell, supra, at 124–130 (opinion of Black, J.), 155 (opinion of Harlan, J.), 293–294 (opinion of Stewart, J.).

Likewise, Alito is not persuaded here, and stresses that many fractured opinions have much precedential weight–including Justice Powell’s Bakke plurality.

Nor can it be correct to say that “Harris in no way strengthens the force of stare decisis in this case” because a “ ‘majority of the Court expressly disagreed with the rationale of [a] plurality.’ ” Ante, at 3–4 (SOTOMAYOR, J., concurring) (quoting Seminole Tribe of Fla. v. Florida, 517 U. S. 44, 66 (1996)). Decisions in which no one rationale commands a majority of the Court—including prominent decisions based on the views of a single Justice—are often thought to have precedential effect. See, e.g., United States v. Booker, 543 U. S. 220 (2005); Regents of Univ. of Cal. v. Bakke, 438 U. S. 265, 269–272 (1978) (opinion of Powell, J.). And, of course, if Harris is not entitled to stare decisis weight, then neither is the Court’s opinion in this case. After all, only four Members of the Court think that the Court’s holding is the correct reading of the Constitution. See ante, at 1–3 (BREYER, J., concurring in part and concurring in judgment).

Alito disagrees with Sotomayor’s approach to stare decisis, and calls her out for changing precedent only because there are the votes to do so.

As she concedes, ante, at 4, JUSTICE SOTOMAYOR’s concurrence is necessarily selective in its discussion of the factors that the Court has previously found to be relevant to the application of stare decisis . . . . In short, other than the fact that there are currently five Justices willing to vote to overrule Harris, and not five Justices willing to overrule Apprendi, there is no compelling reason why the Court overrules the former rather than the latter. If the opportunity arises in the future to overrule Apprendi or the present case—both of which presumably involve “procedural rules . . . that do not govern primary conduct and do not implicate the reliance interests of private parties,” ante, at 2 (SOTOMAYOR, J., concurring)—the precedent the Court sets today will be relevant to the issue of stare decisis.

Wow. Sotomayor responds to Alito’s charge that Harris was overruled only because five justices so voted:

JUSTICE ALITO is therefore mistaken when he suggests that the Court overrules Harris because “there are currently five Justices willing to vote to” do so. Post, at 3, n. *. No doubt, it would be illegitimate to overrule a precedent simply because the Court’s current membership disagrees with it. But that is not a plausible account of the decision today. The Court overrules McMillan and Harris because the reasoning of those decisions has been thoroughly undermined by intervening decisions and because no significant reliance interests are at stake that might justify adhering to their result. Likewise, JUSTICE ALITO exaggerates when he suggests that this case creates an important “precedent about precedent.” Post, at 2. Rarely will a claim for stare decisis be as weak as it is here, where a constitutional rule of criminal procedure is at issue that a majority of the Court has previously recognized is incompatible with our broader jurisprudence. And finally, JUSTICE ALITO’s contention that Apprendi and Harris stand on equal footing for stare decisis purposes, post, at 1–2, 3–4, n. *, is simply inconsistent with our last decade of Sixth Amendment jurisprudence

I suspect the debate between these two over Apprendi will re-emerge in the near future.