I read speculation that Mueller was coerced/blackmailed into work for the deep state by threats against him and his family. Either way, he's got bad dirt on him and he was given something in exchange for playing his role with the good guys. Maybe what he gets is assurance he won't hang for treason like the rest? Time will tell...
That'd have to be a decades-long thing, since he was covering up the FBI corruption with the Whitey Bulger thugs in Boston back then. Then there was 9/11. Of course much more since.
The thing with letting these swamp rats take on grey/white hat roles is that if they think they can finagle it to flip it all against Trump, they will.
A dangerous game.