The X-Men are in a class supervised by Professor X who submits his students to challenges specific to their mutant powers. Then the professor introduces a new member to the team, Jean Grey, who will be known as Marvel Girl. Xavier explains that he built this school for young mutants so they can exercise their skills away from human prejudice. He adds that he is also preparing his students to protect mankind against evil mutants. 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 Angel leaving the team to join the evil mutants causes Professor X to reconsider the existence of the X-Men. Cyclops asks the Avengers for their help to bring him back but only Iron Man can take the call. Through a viewscope, the X-Men watch the airborne battle where the Angel ends up saving Iron Man from a deadly fall. Xavier concludes that his program is not a failure after all.
Professor X sends the X-Men after a mutant to recruit him. The X-Men find the Blob at a nearby carnival and convince him to visit Professor X at their school. The Blob 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.
A freighter attacks the small Republic of San Marco and Professor Xavier discovers that Magneto and his Brotherhood of Evil Mutants are behind this assault. They invade Magneto's new castle and during the battle, Professor X is caught is a small explosion. The X-Men defeat the Brotherhood, and while the villains flee, Cyclops notes that Quicksilver has disarmed Magneto's bigger bomb to protect the local population from a fatal explosion. However the first one has injured the professor and he has apparently lost his mental powers.
After the X-Men have come back unharmed from their second encounter with the Brotherhood of Evil Mutants, Professor X tells them that he never lost his mental powers. The professor used this opportunity as a final exam for their graduation and he announces that they all passed it with great merits.
Under the mind control of the Puppet Master, Professor X commands his X-Men to destroy the Fantastic Four, claiming that they intend to take over the world. During the battle, the Beast destroys the Puppet Master's clay replica of the professor, enabling him to mentally deactivate the Awesome Android. Against the combined efforts of the two teams, the Mad Thinker and the Puppet Master 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.
Contacted by Cyclops, Professor X informs him that he is in a cave in the Balkans tracking down Lucifer, the man who cost him the use of his legs years ago. Some time later, Xavier calls the X-Men to the Balkans with the instructions to defeat Lucifer if ever he fails. When his students face the Avengers who came to destroy the evil threat, the professor convinces them to let the X-Men handle the situation. After they succeed, Professor X lets his foe leave, but stresses that their score is not yet settled.
The X-Men defeat the Vanisher, a mutant who can instantly teleport himself anywhere.
Iron Man seeks the help of the X-Men to locate the Hulk, and Professor X agrees to let him know if they hear about him.
Professor X suggests to Bobby to go to New York and get some distraction.
Thinking that he might be a mutant, Professor X intends to recruit the Sub-Mariner before he joins the Evil Mutants. They sail to Magneto's island and when Xavier realizes that the Sea Prince has refused the Brotherhood's offer, he orders his team to stop the attack.
Professor Xavier and Scott go to State University searching for new mutants but they found none. During their visit, they encounter the Fantastic Four.
Professor X agrees to let the X-Men go to Antarctica to investigate on a strange man and a saber-tooth tiger they heard of in a news report.
When Cerebro detects a being whose powers are extremely strong, Professor X asks the X-Men to find him before Magneto recruits him. As it turns out, the alien was seeking specimens to take to his home world and so he leaves the planet with Magneto and the Toad.
As the X-Men prepare against an assault by a very powerful mutant, Professor X informs them about his own youth. After her mother had remarried with Dr. Kurt Marko, an ambitious and greedy colleague of her late husband, Charles had to endure the cruelty and bullying of his step-brother Cain. His mother had died soon after and left him with his step-family. An accident triggered by Cain had caused Dr. Marko's death. And in his last breath, he had confessed to Charles that even though his father's death was truly an accident, he could have done more to prevent it. He also warned him about his power and about his son Cain. Xavier remembers how he had discovered his mutant mind powers and how Cain had grown jealous of him. Later, during the Korean War, Cain had decided to desert to a temple and Charles had watched him when he found the Crimson Gem of Cyttorak that turned him in to the Juggernaut. In the present, after Professor has finished telling this tale and the Juggernaut has torn through each of the barriers they set up around the school, the two step-brothers finally come face to face again.
Seeing that the Juggernaut seems impervious to all attacks from his X-Men, Professor X mentally contacts the Human Torch to get his help. Under Xavier's orders, the Torch distracts and blinds the villain with his flame so that the Angel is able to remove the Juggernaut's Psionic Helmet, allowing a mental assault from Professor X who makes him unconscious. Before he leaves, Professor X also erases all memories of what has occurred from Johnny's mind.
On Reed Richards and Sue Storm's wedding day at Baxter Building, Professor X sees Mole Man and his subterranean slaves emerging from the ground to attack the place so he summons his X-Men who manage to push the enemy back whence they came. 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.
When Dr. Bolivar Trask declares to the media that mutants are posing a threat to human kind, Professor Xavier organizes a television debate with Trask to prevent further mutant hatred in the public. During the broadcast, Trask loses control of his Sentinels, so he summons the X-Men to handle the thread before the anti-mutant robots create more of their kind and become rulers of the human race. The Beast is captured during the X-Men's assault on the enemy fortress and, under Dr. Trask's Psycho-Probe, he reveals elements about his past and how Professor X convinced his parents to let him take him under his wing. Then Xavier intervenes to prevent Hank from revealing compromising details. Remembering the Sentinel who collapsed earlier, the professor goes back to the studio to find out why. Then he takes a giant crystal to the fortress where its interference causes all the other Sentinels to collapse. 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, Professor X visits the wounded X-Men at the hospital. Then he and Cyclops head back to his school to join the Angel who is expecting a visit from his parents, 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. When he realizes that Magneto has captured Warren's parents, he mentally contacts Iceman who is recovering after the administration of a new type of drug and sends him to their rescue. Then he probes Magneto's mind and learns that he escaped the Stranger's prison planet by repairing a useless ship. 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, informed of Magneto's escape by the professor, arrives on Earth to take the villain back to his prison planet.
