Jean Grey is welcome to a school for mutants by Professor X who introduces her to the X-Men whom she is joining. She takes the opportunity to show the team his skills at telekinesis. When the Beast tries to kiss the young woman, the X-Men discover that she is not totally defenseless. Next day, when Magneto threatens to take Cape Citadel by force, Professor X sends the team on a mission to stop the mutant with magnetic powers. The young heroes combine their skills to dodge Magneto's attacks and chase the villain away from the base.
Marvel and the other X-Men confront and defeat Magneto's Brotherhood of Evil Mutants for the first time when the villains take over the small Republic of San Marco. They invade Magneto's new castle and during the battle where they defeat the Brotherhood, Cyclops notes that Quicksilver has disarmed Magneto's bomb to protect the local population from a fatal explosion. Unfortunately, Professor X has been injured and he has apparently lost his mental powers.
While Professor X is recovering from his recent injury, Jean gets a short but unexpected visit from her parents at Xavier's School for the Gifted. The X-Men once more engage in battle against the Brotherhood of Evil Mutants who are forced to escape from their space station. As they come back unharmed, Professor X tells them that they passed their final exam with great merits.
On Professor X's order, the X-Men reluctantly attack the Fantastic Four, who he says are planning to take over the world. But when they learn that the Mad Thinker and the Puppet Master are behind this attack, the two teams join their efforts and the villains are forced to escape.
The X-Men are celebrating their graduation day and Professor X appoints Cyclops as their group leader while he is away attending other matters and everybody is happy with his choice. The Brotherhood and their latest recruit challenge the X-Men to a fight, but due to Magneto's cruel inconsideration toward him, the Blob decides not to join Evil Mutants after all.
Hank announces that he is quitting the X-Men because he was unfairly assaulted by the mob. The team fails to stop a mutant criminal called Unus the Untouchable. The Beast rejoins the team with an invention that excessively increases Unus's powers, and forces the villain to promise not to join Magneto before changing him back the way he was.
Xavier calls the X-Men to the Balkans with the instructions to defeat Lucifer if ever he fails. They stumble upon the Avengers who came to destroy the evil threat and engage in battle until Professor X convinces them to let the X-Men handle the situation. While Lucifer is kept unconscious by the professor, the young heroes disarm the bomb and end his threat.
The X-Men defeat the Vanisher, a mutant who can instantly teleport himself anywhere.
The Angel's sudden decision to leave the X-Men and join the evil mutants shocks the team. Through a viewscope, they watch the battle between Iron Man and the Angel who regains his senses in time to save his opponent for a deadly fall.
The X-Men are trying to recruit the Blob, an obese mutant who performs in a carnival sideshow. The Blob meets Professor X at their school, but he refuses to join the team and escapes. When he comes back with carnies to attack the young mutants, Professor X wipes the intruders' memory of the event to protect the X-Men and their school.
The Angel and Marvel Girl are preparing to go on a date.
Thinking that he might be a mutant, Professor X takes the X-Men on a mission to recruit the Sub-Mariner before he joins the Evil Mutants. They sail to Magneto's island and confront the Brotherhood. Xavier realizes that the Sea Prince has refused the Brotherhood's offer and he orders his team to stop the attack.
After hearing a news report about some strange man accompanied by a saber-tooth tiger seen in Antarctica, the X-Men decide to investigate. There, they discover an underground prehistoric jungle called the Savage Land and inhabited by primitive warriors who capture her, and then the Angel, who was trying to locate her. Thanks to Ka-Zar and his faithful pet Zabu, the X-Men find and deliver them from the Swamp Men.
Professor X asks the X-Men to find an extremely powerful being Cerebra has detected before Magneto recruits him, but they find that the Brotherhood of Evil Mutants has already met the Stranger. They are relieved when the alien leaves the planet with Magneto and the Toad as mutant specimens.
As the X-Men prepare against an assault by a very powerful mutant and watch him tear through every barrier they set, Professor X shares memories from his past which is closely connected to their new foe. The Juggernaut seems impervious to any moves from the X-Men who is determined to destroy his step-brother Charles. But with the help of the Human Torch, they manage to remove the Juggernaut's Psionic Helmet, allowing a mental assault from Professor X who makes him unconscious.
On Reed Richards and Sue Storm's wedding day at Baxter Building, Professor X summons his X-Men who manage to push the Mole Man and his subterranean slaves back to their underground world. While the battle rages on, Reed Richards uses a machine that transports all their enemies back to the recent past with no memory of what occurred. Finally, Reed and Sue are wed in front of all their family and friends.
The X-Men have to cut their vacations short when Dr. Bolivar Trask loses control on his army of Sentinels. They launch an attack on the enemy's fortress but eventually get captured by the anti-mutant robots. Thanks to Professor X's science, the Sentinels collapse due to the interference of a giant crystal. The X-Men make a narrow escape from the fortress which the remorseful Dr. Trask has set to destroy along with all his work.
In the aftermath of the battle with the Sentinels, Marvel Girl visits the Beast at the hospital and expresses her worries that she has no news from Professor X, Cyclops and the Angel. Learning of Iceman's critical condition, they both head for their school to inform their teammates, but when they arrive, they are subdued by Magneto who locks them all into a hot air balloon and sends them up to suffocate in orbit. With Cyclops and Marvel Girl's combined efforts, the X-Men manage to get the balloon back to the ground where they join Iceman who is struggling against Magneto. The fight ends when the Stranger arrives on Earth to take the villain back to his prison planet.
