The Dawoodi Bohra are a Shia Muslim sect; many of its members believe that, among other things, boys and girls must be circumcised. The federal government charged some Dawoodi Bohra under the federal ban on female genital mutilation; one of the defendants' main defenses is that they engaged only in symbolic nicking or scraping that left no lasting damage to the girls, and that they should therefore be exempted under the Federal Religious Freedom Restoration Act from the federal statute.

But this defense hasn't yet been explored by the court, because the court instead held that the federal female genital mutilation ban exceeds the federal government's enumerated powers; if such a practice is to be restricted (with or without a religious exemption for relatively harmless symbolic action), it must be done by the states, or through a federal statute that contains a suitable basis for federal jurisdiction (such as travel across state boundaries). The court therefore dismissed most of the charges in the federal indictment The Justice Department initially filed a notice of appeal, but, then dropped the appeal:

On further examination, the Department reluctantly agreed with [the court's] determination, provided notice to Congress under 28 U.S.C. § 530D that it would not challenge the district court's ruling, and proposed a statutory amendment that the Department urged Congress to enact.

When the Justice Department's plans were announced, the House of Representatives intervened to defend the constitutionality of the statute, and Friday the Justice Department filed its opposition. Much of the debate has to do with whether the House generally has the statutory authority to intervene to defend federal statutes that the Justice Department has chosen not to defend. But a key part specifically has to do with whether the House can try to reinstate a federal prosecution that the federal prosecutors have chosen to drop:

Let us be clear at the outset what power the House of Representatives asserts: the House claims that it is entitled to keep alive a criminal prosecution that the Executive Branch no longer wishes to pursue on appeal. Never before has either House of Congress attempted, or any court authorized, such an exercise of core executive power. Article II vests executive power in the President, U.S. Const. Art. II, § 1, cl. 1, and requires that he "take Care that the Laws be faithfully executed," id. § 3. Under our separation of powers, Congress—let alone a single House—cannot intervene and assume control of litigation, simply because it disagrees with the manner in which the Executive has chosen to execute the laws.

I find this separation-of-powers analysis—which I quote in much more detail below—pretty persuasive, though perhaps the House's reply may bring me around. (The House's original motion only talked about the statutory question, as it was entitled to do; now that the Justice Department has brought up the constitutional question, the reply brief is the right place for the House to respond to it.)

I generally sympathize with the view that, when the Justice Department or a state Attorney General declines to defend a federal or state statute in court, there ought to be some means for someone else to defend the legislative will (or, for an initiative, the popular will). In some situations, that might well be possible: For instance, if I sue in federal court to challenge a state statute, and the state decides to concede the statute's unconstitutionality, the case remains in court and the judge still has a legal decision to make: It might make sense for legislators, for instance, to file an amicus brief urging the court to reject my challenge, even though the state and I agree. The state has no unilateral power to enter a judgment in my favor; that is up to the court.

But I think the federal Justice Department does, under federal separation of powers principles, have the unilateral power to choose not to seek an indictment. It likewise, I think, have the power to choose not to try to reinstate an indictment that a district court has dismissed.

I don't think the matter is open and shut, and there's been some debate about the degree to which the federal government's ability to stop prosecuting a case, by dismissing charges, can be constrained; Federal Rule of Criminal Procedure 48(a) allows such dismissals only "by leave of court," but courts have concluded that this judicial supervision must be quite limited, precisely because of the separation of powers:

[U]nder our system of separation of powers, the decision whether to prosecute, and the decision as to the charge to be filed, rests in the discretion of the Attorney General or his delegates, the United States Attorneys.

Still, on balance it seems to me that Congress—and certainly one branch of Congress—cannot step in to try to reinstate a federal prosecution. To quote a Seventh Circuit decision in favor of a prosecutor's power to drop charges,

The government wants to dismiss the civil rights count with prejudice, and that is what Bitsky wants as well. The district judge simply disagrees with the Justice Department's exercise of prosecutorial discretion. As he explained in his response to the petition for mandamus, he thinks the government has exaggerated the risk of losing at trial: "the evidence was strong and conviction extremely likely." The judge thus is playing U.S. Attorney. It is no doubt a position that he could fill with distinction, but it is occupied by another person.

Here is more from the Justice Department's argument: