Season 3

X-Men and the Brotherhood deal with the aftermath of the world finding out about mutants. The Institute is blown up, and Mystique posed as Prof. X to blow it up. Some of the X-Men and Brotherhood are captured, leaving the mutants that escaped to find them and the Professor.

Rogue and Wolverine duck a squad of soldiers when the nationwide alert goes out against mutants, while Storm and Beast go into a meeting of Congress to defend themselves. Meanwhile Juggernaut goes on a rampage and the X-Men feel obliged to take him down.

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.

Wanda goes searching for Pietro. Meanwhile the brotherhood's members are expelled from school, much to Lance's dismay.

Mystique escapes from imprisonment while the X-Men repair and rebuild the Institute. Disguised as Alex, she lures Scott into a trap - leaving him stranded in the middle of the Mexican desert without his glasses.

Evan enters an extreme Skateboarding competition, and puts his skills to the test. But something is wrong: A mysterious woman is watching and following him during the competition.

Wanda receives a clue from one of Magneto's minions, Pyro, directing her to a ski resort. Meanwhile, Kurt is meeting Amanda's parents for the first time, and the Toad believes he can use Kurt's holo-inducer to disguise himself and win Wanda's love.

Rogue begins to lose control of all the people she's ever absorbed as they fight to take over. She discovers unsettling information about Mystique. Scott and Jean go on a date... or do they?

Mesmero mentally controls Gambit into stealing half of the Spider Stone from Angel.

A mysterious female assassin terrorizes the X-Mansion, knocking out the X-Men one by one. Wolverine finds out that it is his clone, created by the Dr. Deborah Risman and raised without love by HYDRA, and she wants to kill him because she holds him responsible for her miserable life. Wolverine and X-23, as she is called, square off in a battle that Wolverine does not want to win.

As Jean's and Scott's graduation day approaches, Rogue suddenly leaves the mansion.

As all the monsters in the tomb attack, the teammates fight to survive and find a way out.

The X-Men are on vacation with Storm as their guardian. Amara falls ill while on the ship.