Plot advice needed: Building stakes for 'chosing sides'.
This sounds like a "secret" waiting to be revealed.
The original framing: this could have happened because the hero being framed was trying to keep a secret for a person they hold dear/important. They were willing to take the fall in order for the secret to stay hidden.
Then things changed. There is now a risk the secret is about to come out into the open. In the days to come the escaped hero gets involved in a fight against 'bad guys', giving him some credit for his 'good behavior'. He gets away before the heroes arrive, they get the tail end of the fight. Investigation of the scene reveals there is something else going on, clues point to a [place/thing/people/organization] the escaped hero is trying to get to.
Follow clues, go to place: here the heroes encounter sudden resistance in a surprise fight from enemies unknown. Escaped hero makes appearance, helps in the fight, disappears via MacGuffin plot device. Plot thickens. (Dun, dun, DUNNN!) More clues, this time about intentions and orders, and perhaps even some sinister Mastermind.
Again, follow clues, go to next place: arrive just in time to have the Escaped Hero confront the Master Villain, and expose the 'secret' he was hiding. Master Villain has a good reason for exposing it (profit/vengeance/bad hair day). Cue in climactic last fight.
Optional Kicker 1: secret is actually a lie, and Escaped Hero had been deceived all these years. However, exonerating evidence allows for a retrial and his freedom.
Optional Kicker 2: 'Master Villain' is actually on a lieutenant, the real 'Master Villain' is still on the loose, and has further plans in the oven.
Optional Kicker 3: Escaped Hero has been mind-controlled all this time. He is being used as a patsy to get closer to the team so the Master Villain has an 'inside man'.
Recipe:
Add personality seasoning to taste, sprinkle in a few well-meaning NPCs, cook for an hour at 375, makes for two plot servings.
All jokes aside, this is all in generic terms so you can add to any background or history you like. Flesh it out to your taste. =)