When the Morlocks create a new sports drink that's harmful to mutants, it finds its way into Spyke's hands at a Skateboarding Competition. To make matters worse, Spyke's powers are becoming more and more uncontrollable and his temper is following suit. Meanwhile Kitty learns to drive, horrifying her worried fellow mutants.
While the X-Men work to restore Xavier's Institute after its devastating destruction, Mystique manages to break free of her incarceration. She soon sets a plan in motion that leads Cyclops into a deadly trap.
When the Brotherhood is expelled from school with nowhere else to go, Magneto sends Gambit to get them to join his side. Meanwhile, Wanda gets her brother Pietro arrested and Magneto sends Gambit and his new recruits to break his son out of jail.
Now that the world knows about mutants, Professor Xavier urges the X-Men and the Brotherhood's return to school to convince their peers they pose no threat. However, the school's Principal Kelly has other plans for the student mutant population.
Storm and Beast step in front of the Senate and try to curb rampant anti-mutant racism. The X-Men fight have to stop Juggernaut, who was unleashed by Mystique and is threatening to destroy a dam.
The remaining X-Men and Brotherhood members go to Area 51 to save their captive members. However, when Cyclops traps the treacherous Mystique in Area 51 to blackmail her into saying where Professor X is, the squads split. The X-Men are now alone in a world which shuns them.