Professor X detects a new mutant and sends the X-Men to investigate. They arrive at a carnival and encounter the Blob, a very fat sideshow attraction who can bounce bullets off of his malleable hide as well as anchor himself to the earth and become immovable. The X-Men bring him back to the mansion as a potential member but the Blob spurns their invitation and returns to the carnival. Realizing that the Blob knows their secret, the X-Men lure him back to the mansion where Xavier wipes his memory.
Magneto and his new Brotherhood of Evil Mutants steal a freighter and use it to take over the South American nation of Santo Marco. The X-Men invade and take the country back. Xavier is caught in an explosion and loses his mental powers.
With Xavier's mental powers gone, the X-Men try to decide how they will function without his leadership. Trying to ferret out the X-Men, Magneto has the Toad enter an athletic event where he leaps to victory. With the crowd turning hostile due to the Toads amazing abilities, the X-Men arrive on the scene to capture him. Magneto snags Angel and whisks him away to Asteroid M. In an attempt to trade the Toad for Angel, the X-Men arrive on Asteroid M where they battle the Brotherhood once again. On their safe return to Earth, Xavier reveals that his power loss was a ruse to test his students.
Xavier reads a news story about Namor and wonders if he is a possible mutant. Magneto comes to the same conclusion and invades the Sub-Mariner's realm with an invitation to join his Brotherhood. Enchanted by the Scarlet Witch, Namor agrees. The X-Men attack and, during the ensuing battle, Namor decides not to join either team, mutant or no.
The X-Men graduate from Xavier's school. The Professor says he is taking a leave of absence and puts Cyclops in charge. He shows him his new mutant-detecting machine, Cerebro. Magneto finds the Blob and invites him to join the Brotherhood. During a scuffle, Xavier's mental blocks dissolve and Blob remembers the secret of the X-Men. The Blob's name lights up on Cerebro and Scott calls the X-Men back to battle the evil mutants. During the battle, Magneto shoots missiles at the X-Men, even though the Blob is in the line of fire. The Blob, feeling betrayed, decides to return to carnival life.
After being attacked by a mutant hating crowd, Beast gets fed up and quits the X-Men. He becomes a professional wrestler but meets Unus, a mutant who cannot be touched. Unus is trying to join Magneto's Brotherhood so he takes on the X-Men. The X-Men barely fend him off and find Beast has constructed a machine that will actually increase Unus' powers. The X-Men try to prevent Hank from using the machine, but, once Unus has been zapped, he finds that he cannot even eat without the food being repelled out of his hands. Beast returns him to normal and Unus promises to will steer clear of Magneto.
Xavier has tracked down Lucifer, who cost him the use of his legs, but finds his foe's heartbeat is rigged to a giant thermal bomb. The X-Men arrive in Bavaria and run across the Avengers who have also just arrived. The X-Men have to stop the Avengers from defeating Lucifer since by defeating Lucifer, the world will be destroyed. After Xavier gives Lucifer a mind blast that renders him unconscious, he contacts his team for help and the Avengers agree to let the X-Men clean up the current crisis on their own. Cyclops uses his eye beams to disable Lucifer's thermal bomb.
Even though he is not a mutant, Xavier allows the X-Men to travel to Antarctica and enter the Savage Land to investigate the noble savage, Ka-Zar. They end up having to save Jean and Warren from being sacrificed by the savage Swamp Men.