While I don't particularly want a prolonged arc about John losing/regaining his powers or anything I will say that I think a temporary, or even feigned, experience with his powers being gone could be a world of good.

A while ago I posted saying that John can't experience change until he finds himself in a position of weakness being protected by those stronger than him. Right now he's on good terms with people but to his perspective there's no reason to believe that it's not fueled by fear. If he loses his powers (even if temporarily) or fakes having lost them to see how people react it could finally be what's needed to get John and all the other students legitimately on the same side. Not just united against a common enemy but instead actually realizing that everyone else has had a lot of issues that they'd had to work to overcome and accepting and realizing that about each other.