It seems impossible to fully figure out Mueller's true agenda without understanding RR.
The way I understand it, this is intentional. Q doesn't want to reveal if he is a "bad guy". The circumstances point to two different extremes.
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An intentional plot to go after Trump. RR appointed special council for malicious reasons. Building legitimate cases(Especially if no real crime) is secondary to framing/leaking/getting info/political impeachment.
The fact that he hasn't been fired, plus his history with General Cartwright is the main hole in this. His history seems to be that of a "good guy" who wouldn't ever consciously take part in something like this.
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The Mueller investigation is ultimately there to take down those who plotted against Trump (Indirectly, as the OIG will probably be bringing the majority of serious charges). The Mueller team is one big honeypot. Partisans were chosen intentionally. They are made to feel as if they are running the show, but they are actually being highly monitored. The extreme partisan nature of the hires makes a legitimate court case unwinnable, therefore protecting Trump. The OIG builds real cases in the mean time.
There are a bunch of problems with this as well. The perception of what has happened to people like Manafort, yet not seeing the same with the people who were around him doing the same exact thing (Tony) indicates the Partisan makeup of the team is doing exactly what you expect: Protect D's and hurt R's.
On top of that, there seems to be 3 different categories of people that were at the top of the FBI.
Those who still have a job. (RR/Bill Priestap)
Those who have been chained to a desk (Bruce Ohr, Lisa Page, Peter Strzok) (probably cooperating witnesses)
Those who have been outright fired. (probably fucked)
Occam's razor suggests RR is a "good guy", but I guess Q doesn't want us to know for sure.