Again the X-Men are seen in a training session. Marvel Girl’s task is to telekinetically open a box and take out its content – a birthday cake. Xavier says that it has been one year since classes started at the school and he felt that the date should be celebrated.
Meanwhile four other mutants are seen having dinner. They are the hopping Toad, the illusionist Mastermind and the siblings Quicksilver and Scarlet Witch. Pietro is a speedster, while Wanda causes strange reactions by pointing with her fingers. Mastermind tries to impress the beautiful witch, but she is not interested and her twin brother stands up for her as the disgusting Mastermind threatens her.
At the same time Magneto, the group‘s leader is seen stealing a large freighter. Using his magnetic powers he alone drives the ship to the secret hideout on an atlantic island. Upon his return the loyal Toad tells him about the fight between Quicksilver and Mastermind. The siblings want to leave the group, but Magneto reminds them that they are forever in his debt. A flashback scene shows that he saved the Scarlet Witch from an angry mob after she accidentally caused a barn to burn down in their native village in europe.
Magneto and his Brotherhood use the single freighter to attack San Marco, a small nation in South America. As Xavier learns about the incident from the newspaper, he contacts Magneto with his telepathy. They dispute their different views; Xavier preaches coexistence with humanity, while Magneto thinks that mutants are superior and as such have the right to rule.
After the contact ends, the Brotherhood continues their invasion. Mastermind creates an unlimited illusionary army and the natives are very frightened. Within hours the whole country is taken over and Magneto names himself the ruler.
Professor Xavier and the X-Men cross the border of San Marco under the cover of an american professor and his students being on a goodwill visit. Once inside the country they switch into costume and attack Magneto’s palace from different sides, yet they are unfamiliar with their opponents powers and as a giant fire front appears they X-Men run.
Xavier senses his students panic and enters the palace himself. He shows them that the firewall is an illusion by wheeling through unharmed. Together they plan to confront the Brotherhood in the main tower, but the door has been booby-trapped with a bomb. In the last instant before the Beast opens the door, Xavier senses the danger and hurls himself in the way taking the brunt of the explosion.
The Brotherhood uses an escape slide to make their way to their freighter, but shortly before leaving Quicksilver disarms a second bomb that Magneto had designed to destroy the whole country of San Marco (along with the X-Men).
As Xavier regains consciousness he discovers that his mental powers were damaged by the bomb blast he took.