For Mueller, a Feared Weakness Becomes a Strength

By contrast, after Mr. Trump fired Mr. Comey in May from his subsequent job as F.B.I. director and Mr. Rosenstein appointed Mr. Mueller as special counsel, Mr. Rosenstein invoked the regulation — meaning he retained supervisory control.

At the time, some Democrats greeted that arrangement with suspicion. They worried that Mr. Rosenstein — a Trump appointee who had helped with Mr. Trump’s firing of Mr. Comey by writing a memo criticizing Mr. Comey’s handling of the Hillary Clinton email investigation — would keep Mr. Mueller on a short leash.

During a June hearing, for example, Senator Kamala Harris, Democrat of California, pressed Mr. Rosenstein to instead create a more independent special counsel who could oversee himself, like Mr. Fitzgerald.

“Are you willing to do as has been done before?” she demanded.

Mr. Rosenstein demurred. While noting that Mr. Bush could have fired Mr. Fitzgerald for any reason — so working under the regulation gave Mr. Mueller greater protection — he also said there were other complicated legal issues that led him to his decision. (One of the complexities may have been that Mr. Mueller was not a current Justice Department employee at the time of his appointment, unlike Mr. Fitzgerald in 2003, so Mr. Mueller most likely could not have been delegated attorney general supervisory powers, Mr. Katyal said.)

The anxieties of that period make it all the more striking that, 10 months later, Mr. Mueller’s team is stressing his subordination to Mr. Rosenstein to repel Mr. Manafort’s attack.

Still, several specialists cautioned that Mr. Mueller’s subordination could revert to a weakness if Mr. Trump were to fire Mr. Sessions or Mr. Rosenstein, putting someone else in charge of the special counsel.

Against that backdrop, Julie O’Sullivan, a Georgetown University law professor and a former federal prosecutor, worried about the lengths the filing went to in detailing Mr. Rosenstein’s approval for Mr. Mueller’s actions.

“Mueller’s lack of independence was viewed as a real problem, but now it’s a response to any attack on the indictment,” she said. “I do wonder, though, if he hasn’t put Rosenstein in additional jeopardy.”