Mueller is a black hat version- Flynn was framed to put pressure on him to get to POTUS, for the fact that Flynn knew too much and for vengeance by McCabe because Flynn testified on behalf of the female FBI agent that sued McCabe.
Mueller is a white hat version- Flynn was charged to give the conspirators a false sense of security because (a) Flynn is out of the way and (b) Mueller is their guy. But in reality, Flynn never left the team, helped guide the white hats, the house/money/bankruptcy stuff was all part of a movie, the judge will allow the guilty plea to be withdrawn, Flynn will be publicly cleared and testify against the black hats.