The X-Men are in a class supervised by Professor X and Cyclops exercises his mutant eye beams against the Beast and Iceman. Then 'Slim' Summers and the team are introduced to a new member, Jean Grey, who will be known as Marvel Girl. Next day, when Magneto threatens to take Cape Citadel by force, Professor X sends the X-Men 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.
Cyclops tells Professor X about his constant fear that he might accidentally cause serious harm to someone he loves with his optical blasts. 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.
Cyclops 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.
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. Xavier introduces Scott to Cerebro, a machine able to detect other mutants. 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.
Cyclops questions his own leadership when Hank announces that he is quitting the X-Men because he was unfairly assaulted by the mob. The team tries to stop a mutant criminal called Unus the Untouchable but even Cyclops's optic blast can't reach him. 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. Cyclops tries go get help from the Avengers but only Iron Man takes the call. Through a viewscope, the X-Men 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 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.
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.
The X-Men pursue the Brotherhood of Evil Mutants who attacked them to their submersible fort, but they manage to get away. The X-Men track down Magneto to his fort, forcing him to flee while his underwater lair is destroyed by a mysterious captive.
Professor Xavier and Scott go to State University searching for new mutants but they found none. During their visit, they encounter the Fantastic Four.
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. They meet Ka-Zar and his faithful pet Zabu who helps them rescue Marvel Girl after she was captured by the Swamp Men, a tribe of primitive warriors.
While looking for a strong being detected by Cerebro, Scott unwillingly causes a riot in the city streets as a policeman removes his special sunglasses. After realizing that the Brotherhood of Evil Mutants has already met the Stranger, they engage in a battle and the Stranger decides to teleport elsewhere, taking Magneto and the Toad along. After Cyclops helps Quicksilver who has been frozen by Iceman, the siblings declare that they will never serve Magneto again, but refuse the X-Men's offer to join them. All 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. Cyclops gets a mild injury during their escape.
In the aftermath of the battle with the Sentinels, Cyclops is taken to a hospital where he is forced to demonstrate to an optometrist what would happen if he tried to examine his eyes. Then he and Professor X head back to their school to join the Angel, but as they arrive, they are subdued by Magneto who locks the X-Men 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.
