People seem to like the new arc idea so I'm putting my idea here
Story arc with branching path:
You succeed - You're given a permanent temp power of a flying hoverboard that was found in the bad persons warehouse as it was cleaned out.
You fail - You're captured and put in a containment building after having your powers disabled in a way that vaguely matches your origin, and the only way to escape is using a hoverboard you find there, which you keep after.
Now varry this idea throughout the game with other (new, not re-gating) powers, costume peices, and even unique enhancements