Mr. Mueller’s original assignment from Mr. Rosenstein was to look into Russian meddling in the 2016 election and any links to Trump campaign officials, with the ambiguous addition of “any matters that arose or may arise directly from the investigation.”
In a response this week, Mr. Mueller’s team insisted that Mr. Manafort’s Ukraine dealings, in light of his campaign role, were relevant to investigating links between Russia and the Trump campaign. The team also argued that Mr. Manafort had no right to challenge Mr. Mueller’s jurisdiction. (It did not, however, invoke the widespread belief that Mr. Mueller is using the Ukraine charges to pressure Mr. Manafort to divulge what he knows about 2016 events as part of a plea bargain.)
But members of Mr. Mueller’s team also backed up those arguments with a striking move: They emphatically pointed to their subordination to Mr. Rosenstein — the acting attorney general for the Russia investigation because Attorney General Jeff Sessions is recused from it.
While Mr. Rosenstein has testified that he knows about and approves of what Mr. Mueller is doing, the filing went into significant new detail, including disclosing that Mr. Rosenstein wrote a memo on Aug. 2 blessing the idea that Mr. Mueller’s jurisdiction extends to Mr. Manafort’s Ukraine-linked dealings.
“The acting attorney general appointed the special counsel, defined his jurisdiction, understands the scope of his investigation and has specifically confirmed that the allegations that form the basis” of Mr. Manafort’s prosecution are within Mr. Mueller’s purview, the filing said. “In these circumstances, no serious question of political accountability can be raised.”
Mr. Mueller’s assertive use of a Trump appointee’s control over his investigation as a shield against Mr. Manafort’s attack was a remarkable moment in the history of recurring tensions over the independence of investigations touching on high-level executive branch officials.
After the Watergate scandal, in which President Richard M. Nixon forced the Justice Department to fire the prosecutor investigating him, Congress enacted a law permitting the appointment of an “independent” counsel who would report to a panel of judges rather than to a presidential appointee.
Although the Supreme Court upheld Congress’s constitutional power to make that arrangement in a 1988 case, both political parties came to see it as a bad idea. In 1999, when the independent counsel statute expired, lawmakers did not renew it.
As a replacement, the Justice Department created a regulation to permit the appointment, from outside the government, of a special counsel who would exercise day-to-day independence but remain subject to control by the attorney general, who could veto decisions like whether to file charges or expand jurisdiction. At the same time, it limited the attorney general’s power to fire a special counsel to cases of misconduct.
But that regulation has rarely been used. The most high-profile case arising during George W. Bush’s administration — the appointment in 2003 of Patrick J. Fitzgerald to investigate who leaked the identity of Valerie Plame Wilson, a C.I.A. official — bypassed its envisioned arrangement.
Mr. Fitzgerald, then a United States attorney in Chicago, was appointed as a special counsel by James B. Comey, then the deputy attorney general, after Attorney General John Ashcroft recused himself from the investigation. Mr. Comey also delegated his supervisory powers as the acting attorney general to Mr. Fitzgerald, permitting the prosecutor to take major investigative steps “independent of the supervision or control of any officer of the department.”
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.”
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