First, most simply, Trump could order Mueller fired. Our Constitution gives the president the full prosecution power in Article II; accordingly, any federal prosecutor works ultimately for the president. That constitutional reality is not something we could write around with a regulation. Instead, we opted to try to focus accountability for any such activity. The regulations provide that Mueller can “be disciplined or removed from office only by the personal action of the Attorney General” (again, Rosenstein here, because Sessions is recused) and only for “good cause.” The president therefore would have to direct Rosenstein to fire Mueller — or, somewhat more extravagantly, Trump could order the special-counsel regulations repealed and then fire Mueller himself. Either of those actions was unthinkable to us back in 1999, for we understood that President Richard Nixon’s attempt in this regard ultimately led to his downfall. At the same time, after Trump’s firing of FBI Director James B. Comey this month, many things once thought beyond the realm of possibility look less so now.
Second, Congress could muck up Mueller’s investigation. Several congressional committees are looking into Russia, and any one of them could decide to give immunity to a particular witness. You’ve seen the drill before: Some high-ranking corporate executive comes before Congress and refuses to answer a question because it might incriminate her. The way Congress deals with that problem is to say that her testimony can’t be used against her. That’s part of Congress’s truth-seeking function. Formally, such immunity is confined to her congressional testimony and doesn’t prevent criminal charges altogether, again because the Constitution gives the president the prosecution power. But in the real world, if one of the committees gives immunity to, say, former national security adviser Michael Flynn, that could make Flynn’s prosecution impossible. Recall the Oliver North case. North was criminally convicted by an independent counsel during Iran-contra. But the U.S. Court of Appeals for the District of Columbia Circuit threw out his conviction because Congress earlier gave him immunity for his testimony. Even though that immunity didn’t directly cover action by the independent counsel, the court found that the special prosecutor could have benefited from the fruits of that congressional testimony. There is a possible silver lining in this scenario, though: If Flynn was given immunity, he would have to testify, including against higher-ups, as he would no longer have any rights to refuse to testify to protect himself against self-incrimination. So even if Mueller can’t get Flynn, he might be able to convict someone else, including potentially a bigger fish.
Third, the regulations permit Rosenstein to define the scope and powers of the investigation.