The X-Men are in a class supervised by Professor X and Beast exercises his mutant skills in acrobatics and agility against the training machine. Then Hank McCoy and the team are introduced to a new member, Jean Grey, who will be known as Marvel Girl. When he tries to kiss the young woman, he discovers that she is not totally defenseless. 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.
The Beast 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 and everybody is happy with his choice. To mark the occasion, Hank decides to have a night out with his teammate Bobby at a Greenwich Village coffee shop. 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. Taking on a career as a pro wrestler, he discovers another mutant called Unus the Untouchable during a match. Seeing Mastermind in the audience, Hank decides to go back with the X-Men and prevent Unus from joining the Brotherhood. The Beast submits him to 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 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.
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.
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.
Hank has to cut his vacations short when Dr. Bolivar Trask loses control on his anti-mutant army of Sentinels. During the X-Men's strike against the enemy fortress, Iceman the Beast are made unconscious with sleeping gas. Under Dr. Trask's Psycho-Probe, the Beast recalls his childhood when he realized that he had powers, how people used to call him a freak and how his parents accepted Professor Xavier's offer to take him under his wing. After a harsh battle, Professor X neutralizes the Sentinels with a giant crystal and the X-Men make a narrow escape from the fortress which the remorseful Dr. Trask has set to destroy along with all his work. The Beast breaks a few bones in the escape.
In the aftermath of the battle with the Sentinels, the Beast is taken to a hospital where they tend his fractures, but he is healing rapidly. Marvel Girl visits him 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 their 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.
