Magneto steals plans for a top-secret project that produced super soldiers. Wolverine worked on it during World War II.

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.

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.

Wolverine finds his clone, X-23, who's trying to destroy Hydra, her creator, and the two team up to complete the mission.

Xavier finds Apocalypse in Egypt, and Apocalypse unleashes four horsemen, who battle the X-Men.

The battle against Apocalypse rages as X-Men, the Brotherhood, and Acolytes join forces to stop him from turning all humans into mutants.