Xavier detects a powerful entity has arrived on earth and sends the X-Men to investigate. The Stranger tries to acclimate himself to Earth customs but runs across Magneto and the Brotherhood. The X-Men arrive on the scene and battle the Brotherhood, but the Stranger leaves with Magneto and Toad in the conflict. Quicksilver and the Scarlet Witch decide to return home to Central Europe. The X-Men encounter the Stranger again and Xavier realizes he is an alien. The Stranger explains that he has been collecting mutants from across the universe and takes Magneto and Toad away with him into space.
Cerebro detects a powerful mutant and Xavier fears that he knows who it is. The X-Men prepare the mansion for an all out assault. As the mysterious villain batters his way through the mansion's defenses, Professor X tells his students his origin story and how his step-brother changed from tormenting bully to an unstoppable Juggernaut.
The X-Men invade the Sentinel's underground complex but are captured. Beast is taken before the Sentinel's leader, Master Mold, and has his mind probed. Master Mold commands Trask to make an army of Sentinels so they can take over the world.
With the X-Men captured, Xavier heads back to investigate a fallen Sentinel to try and figure out what stopped it. The X-Men escape and battle the Sentinels but it is the timely intervention of Professor X and the self sacrifice of Dr. Trask that stops Master Mold and saves the day.
In the aftermath of their battle with the Sentinels, Hank, Bobby and Scott are taken to the hospital with injuries. Iceman is delirious in a coma but his companions recover quickly. When Warren's parents call and say they are dropping by for a visit, Angel flies back to the mansion where he is attacked by a mysterious stranger. Xavier and Cyclops, worried with no word from Angel, also return home and are attacked. Beast and Jean are the last to show up and are also taken down. As Warren's parents arrive at the mansion, they are greeted by Magneto.
With the rest of the X-Men captured, it is up to Iceman to beat Magneto single-handed and rescue Warren's parents. Xavier ends up calling the Stranger telepathically and the alien chases Maggie off, trying to take him back into space.
Bobby and Hank tussle with mysterious Calvin Rankin, who beats them by mimicking their powers. Calvin then has an encounter with Jean at a restaurant. Realizing he is dealing with the X-Men, Calvin follows Jean home and asks to join them. Once he has absorbed all of their powers, he battles them and captures Jean. The team follows him to his hideout deep in an old mine. Mimic uses his powers to uncover a machine his father built that will allow him to keep the combined powers for good. Xavier allows Mimic to use the machine which doesn't give him powers but strips his mimic powers away.