The X-Men and Brotherhood deal with the after math of the world finding out about mutants. Mystique, diguised as Professor X, manages to blow up the Insitute. Some of the X-Men and Brotherhood were captured, leaving the mutants that escaped to find them and the Professor.

During the rebuilding of the manor, Kitty and Kurt intercept a bunch of graffiti artists disguised as monsters. The older students get to go back to Bayville High for one day before attending a hearing to determine their ultimate fate, while they are banned from using their powers.