The disqualification of two of President Trump’s top prosecutors — Alina Habba of New Jersey and Lindsey Halligan of the Eastern District of Virginia — underscores the precarious position of the 47th president’s Department of Justice as it faces a vexing set of appellate choices. 

Main Justice could just be getting its appellate arguments in order. The administration, though, could also be weighing whether further appeals — and the possibility of adverse rulings — would result in the appointments of prosecutors that Ms. Bondi and Mr. Trump would prefer not assume control of some of the DOJ’s most powerful offices. A Supreme Court ruling constraining the president’s appointment power is one possible negative outcome.       

The disqualification of Ms. Halligan was especially devastating because when Judge Cameron McGowan Currie ruled that Ms. Halligan was unlawfully appointed, she also dismissed the charges she brought against two of the president’s critics — the former FBI director James Comey and New York’s attorney general, Letitia James. Ms. James is also challenging the appointment of the acting United States attorney for Northern New York, John Sarcone.

All three prosecutors — Ms. Habba, Ms. Halligan, and Mr. Sarcone — were unconventionally appointed and lacked confirmation by the Senate, a prerequisite for permanent installation as a United States attorney. Ms. Habba and Mr. Sarcone were retained by Attorney General Pam Bondi even after the federal judges in their districts, as is their discretion, rejected their ongoing service past the 120-day interim period and selected other candidates.

Ms. Halligan’s circumstances were slightly different. She is the second consecutive interim appointment in the Eastern District of Virginia, following her predecessor, Erik Siebert. Both Mr. Comey and Ms. James argued to Judge Currie, with success, that the attorney general lacks the authority to appoint two consecutive interim appointments. 

A similar ruling could soon come down in respect of Mr. Sarcon, who has issued two subpoenas against Ms. James. One is tied to allegations that she violated Mr. Trump’s civil rights when she brought her civil fraud case against him that resulted in a $500 million judgment. The other is related to the possibility that Ms. James violated the rights of a major civil rights organization, the National Rifle Association, when she launched her legal crusade against it and upended its ability to exist in New York.

The government tested the appellate waters in respect of Ms. Habba’s disqualification. In August Judge Matthew Brann, a Republican appointee of President Obama, ruled that “Faced with the question of whether Ms. Habba is lawfully performing the functions and duties of the office of the United States Attorney for the District of New Jersey, I conclude that she is not.” He also determined that “she must be disqualified from participating in any ongoing cases.”  

The DOJ contends that the attorney general possesses  “substantial authority to decide who is executing the criminal laws of the United States,” but on appeal the Third United States Appeals Circuit ruled that such authority did not extend to keeping Ms. Habba in her office. A panel of three jurists concluded that “under the Government’s … theory, Habba may avoid the gauntlet of presidential appointment and Senate confirmation and serve as the de facto U.S. Attorney indefinitely. This view is so broad that it bypasses the constitutional (appointment and Senate confirmation) process entirely.”

Ms. Habba, in a statement following that ruling, declares that “As a result of the Third Circuit’s ruling, and to protect the stability and integrity of the office which I love, I have decided to step down. But do not mistake compliance for surrender. This decision will not weaken the Justice Department and it will not weaken me.” Ms. Bondi colors herself “saddened.”  

Ms. Bondi, in a post on X, also suggests that Ms. Habba, whom she calls a “dear friend,” intends to “return to lead the “U.S. Attorney’s Office for the District of New Jersey” if the government’s appeal on behalf of Ms. Habba prospers. Such an appeal would, in the traditional course, be submitted, after a panel has weighed in, to the full complement of the appellate court and then, possibly, to the Supreme Court.

A losing party has 30 days to file an appeal of a final ruling, but no such appeal has been docketed at the Third Circuit, which handed down its decision last week. Ms. Bondi has also vowed an “immediate appeal” to the disqualification of Ms. Halligan, though no appeal has yet been filed there, either. Instead the DOJ tried to indict Ms. James for a second time, which failed.