Simple concept in my head (or it was simply until I had a migraine, so bear with please). In comics, sometimes you get alternate branch type comics. "What if Spider-man saved Gwen Stacey?" "What if Professor Xavier had been chosen to be the Juggernaut?" "What if Superman had landed in the Soviet Union instead of rural Kansas?" Stuff like that. What If? missions could be something unlocked by working with different hero/villain groups, and would generally pertain to some member of that group, or one of their enemies. I've been out of the loop a while now, so I don't know who is who at this point and thus can't give specific examples of ideas. Obvious choices being things like "What If *upstanding hero* had turned to villainy?" or "What If *tragic villain* had never *tragedy*?"
Admittedly, through the "light is fire" and "knife in brain" part of my migraine, I can't be certain I'm being coherent, but discourse (in the form of points and ideas and such) is always appreciated.