The X-Men are in a class supervised by Professor X and the Angel trains his flying maneuvers and wing reflex against the training machine. Then Warren Worthington III and the team are introduced to a new mutant 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.
An atomic blast hitting the Angel while he flies over Stark's factory causes him to turn evil and he decides to leave the X-Men in hopes to join the evil mutants. Iron Man tries to bring him back but it turns into an airborne fight. The armored hero makes a leap of faith as he overtaxes the power of his jets so they eventually fail him while he is high in the sky. Seeing the hero plummeting to a certain death shakes the evil out of the Angel's mind and the young mutant flies to his rescue.
Angel 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. 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 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.
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.
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.
Angel is contacted by Tanya Anderssen that want him to lead an expedition to the Savage Land to find Karl Lykos
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, the Angel manages 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. As an army of villains are attacking the Fantastic Four, the Angel engages battle with the Black Knight who is trying to kill Daredevil in his maneuvers to take control of a Hydra truck carrying a Vortex Bomb. Unfortunately, the Angel is paralyzed by the Mandarin's Nerve-Ray ring and is caught in mid-air by the Beast and Iceman. 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.
Warren has to cut short his vacations with his parents in Long Island when Dr. Bolivar Trask loses control on his anti-mutant army of Sentinels. They launch an attack on the enemy's fortress but eventually get captured 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.
In the aftermath of the battle with the Sentinels, Angel learns that his parents plan to visit him at his school so he flies off to intercept them while all his teammates are at the hospital. When he arrives at Xavier's school, he is captured by Magneto who locks the X-Men 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. Next day, Warren enjoys some time at school with his family, who has no clue of what occurred.
