Emil Bove III, the acting deputy attorney general, stood stone-faced and alone at the prosecution table inside the federal courthouse in Manhattan last week to do a job his onetime colleagues in the U.S. attorney’s office for the Southern District of New York would not.

Mr. Bove, who runs the day-to-day operations of the Justice Department under President Trump, was there to seek the dismissal of corruption charges against Mayor Eric Adams, a task seen as so dubious that two prosecutors in a prideful office known as the “Sovereign District of New York” resigned rather than carry out his demands to do it.

He lashed out at the office after the hearing. “There are no separate sovereigns in this executive branch,” he wrote in a statement that also suggested his former co-workers prepare to resign if they disagreed.

It was the latest chapter in Mr. Bove’s estranged-family feud with the Southern District, where he rose to prominence as a top terrorism prosecutor and departed in December 2021 after a case he oversaw crumbled over procedural violations by members of his team.

He would go on to become a key member of Mr. Trump’s defense team known for his unyielding style. Since being installed at the Justice Department, he has emerged as one of the most powerful officials in the country and the main enforcer of Mr. Trump’s demands for retribution and unimpeded control of federal law enforcement.

That Mr. Bove, 44, has quashed dissent at the Southern District is an indication of its outsize importance as a symbol of prosecutorial independence — and its enduring role in Mr. Trump’s own long, tortured relationship with the department since his first term. But his forceful tack is also a measure of his own fraught relationship with an office that provided him with the know-how and confidence to now challenge its power and autonomy.