At a maximum-security facility, several surveillance cameras explode as a shadowy figure floats over them. In a nearby cell, two guards pester the Beast, while he sits reading a copy of Animal Farm. Suddenly, several alarms go off and one of the guards runs off. After determining that they are under attack from mutants, the remaining guard points his gun at the Beast, ordering him to call off his friends.

The Beast believes the attacker to be Wolverine, but he is soon proved wrong. As the guards weapons are pulled out of his hands. Next, the cell door seems to come alive and slams through the wall. Where the shadowy figure from before hovers above the Beast. The Beast refers to this man as Magneto. Magneto blasts the Beasts shackles and tells the Beast to come with him. However, the Beast explains that he is waiting for his day in court and that he is confident that he will be set free. Just then, guards open fire from outside of the cell. Magneto erects a magnetic shield inside the cell and scolds the Beast for trusting humans. In the conversation, the Beast reveals that he entered the Mutant Control Agency at Professor X’s behest. As he leaves, Magneto states that the humans must be crushed, and that he has the power to do it.

Outside, he is met by a full compliment of military troops and artillery. Though he easily subdues them with his magnetic powers. Back at the mansion, Professor X is watching news broadcasts of the happening at the prison. Jubilee enters the room and mistakes the broadcast for a movie and comments on the graphics. The Professor then explains that it is a news broadcast and that he knows the man in the picture. He goes on to explain how he and Magneto met. And also how Magneto came to be the vigilante he is today.

Later, the Beast is standing trial. Senator Kelly is questioning the Professor. The Beast asks to address the court and begins to quote a poem, however, he is met with disdain from the people present in the court. Wolverine and Cyclops sit in the stands and watch. After Beast is sentenced, the guards march him back to his cell. As they do, several people scream comments and hurl tomatoes at him. Suddenly, a big hairy mutant begins attacking the humans and hurling benches. Several guards shoot him and Cyclops says that they have to help him. But Wolverine refuses. Hence, Cyclops is forced to do it alone. Later, the Professor uses Cerebro to search for Magneto. Jubilee and Storm approach and Storm questions the Professor about who Magneto is. Suddenly, an alarm goes off. It is Cyclops calling from the Blackbird, asking them to prepare the sickbay for a critically injured mutant. In sickbay, the mutant from the courthouse lies attached to several monitors. Wolverine argues that he must be removed from the mansion. Storm approaches from the hallway and states that, that is the way most of the X-Men felt when Wolverine first joined the X-Men.

Back in the war room, Jubilee states that something about the injured mutant reminds her of Wolverine. Cyclops states that Wolverine has a past with the mutant. On a nearby monitor, Wolverine is seen walking toward sickbay. He enters the mutant’s room and slices the cables connecting him to the monitors. He begins to wheel him out of the room when the Professor stops him.

They are still debating the issue when an alarm goes off. The Professor is positive that it is Magneto. Storm and Cyclops charge off and Jubilee begins to run after them, but the Professor states that she isn’t ready yet! She is instead commanded to stay at the Mansion and watch Sabretooth. Pissed off, Wolverine asks the Professor why they have to fight the Professor’s enemy, but have to go easy on his.

The X-Men track Magneto to a military compound. They attempt to begin a debate with him about the ethics of what he is attempting to do. As he wishes to start an all out civil war between mutants and humans. Though he turns his magnetic powers on them rather than attempting to talk it out.

He goes on to arm the nuclear warhead and launches them. Storm takes it upon herself to destroy them. She flies after them, as she does, she is contacted by Professor Xavier telepathically. He gives her access to Cerebro and she gains knowledge about the missiles. She uses her wind powers to change the trajectory of the missiles, and lightning to short-circuit the warheads. They land harmlessly in the ocean. She collapses and falls out of the sky. Wolverine saves her just in time and they return to the mansion. On a distant hill, Magneto stands, wondering why Xavier has turned against him.