The X-Men are in a class supervised by Professor X and Iceman exercises his mutant skills at creating frozen objects against the Beast then Cyclops. Then Bobby Drake 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.
Iceman 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.
During a day cruise around New York City, the ship is attacked by Captain Barracuda and his pirates so Iceman teams up with the Human Torch to apprehend the villains.
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, Bobby decides to have a night out with his teammate Hank at a Greenwich Village coffee shop. He meets his friend Zelda who works there as a waitress and for whom he has some attraction. 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.
By refining his ice crystals and lowering further his temperature, Iceman can now make his body look like ice instead of snow. Hank announces that he is quitting the X-Men because he and Iceman were unfairly assaulted by the mob after rescuing a child. 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 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. Iceman seals the opening with a solid mass of ice to prevent them from returning. After saving the Angel from a deadly fall, Iceman is simultaneously assaulted by Electro, the Mandarin, the Unicorn, the Melter and the Beetle. 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.
Bobby has to cancel a date with Zelda when Dr. Bolivar Trask loses control of 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 and captured. Freed by his other partners, Iceman and his team take action to stop the Sentinels, but they eventually get captured again by the anti-mutant robots. 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. Unfortunately, Iceman is injured from the heat of the blast.
In the aftermath of their battle with the Sentinels, Iceman is taken to a hospital where he lies unconscious in a very critical and delirious condition. As his state is deteriorating, Dr. Thomas considers using a new type of drug. In his delirium, Bobby questions his importance among the X-Men. The physician finally decides to administer the sulfa drug with a laser-induced hypodermic. Shortly after, Professor X mentally contacts Iceman who is finally recovering and sends him on mission to rescue Warren's parents from Magneto. He manages to stop Magneto's mutant-creating machine and courageously engages the villain in battle, soon joined by his teammates. The fight ends when the Stranger arrives on Earth to take the villain back to his prison planet.
