||With his goal of nuclear Armageddon close at hand, the Mutant Master monitors the X-Men. Cyclops and Iceman were stopped in America fighting the US military in an attempt to stop a gas attack, while Beast, Marvel Girl and Angel are held prisoner in a Russian prison when attempting to stop a bomb plot.
In the States, Cyclops and Iceman fight their way through the military opposition to enter the building where the nerve gas has been planted. Deducing that it has been put into the ventilation system, Cyclops orders Iceman to freeze it solid, preventing the gas from being released. However, they are attacked by Mastermind and Unus, who catch them off guard. While in Russia, Marvel Girl uses her telekinetic powers to pull one of the guards close enough to their cell for Beast to knock him out and take his keys. Freeing themselves the X-Men disrupt a meeting of Russian military officials in order to stop a bomb planted in their meeting table, however the Blob (who was also in the same cell as them) has revived and appeared to oppose the X-Men from succeeding in their task.
Back in the States, Cyclops and Iceman continue to battle Unus and Mastermind. While the two evil mutants have the upper hand, Cyclops and Iceman turn the tables when Cyclops causes a dense fog when he melts some of Iceman's ice formations with his optic blast. Unable to see their foes and with the military fast approaching, the two evil doers flee the scene, as do the two X-Men who escape in their stolen Factor Three flying saucer. The military arrive to find the room empty and their base undamaged. As Cyclops and Iceman flee the scene, they consider their mission accomplished.
While back in Russia, the X-Men are in a Mexican stand-off with the Blob who holds the briefcase filled with explosives in front of the X-Men. The Blob boasts how the bomb can have no effect on him, however Marvel Girl psyches the Blob out, putting enough doubt in the Mutant Master being truthful about the strength of the bomb to cause the Blob to flee the scene in fear, dropping the bomb. Angel quickly grabs it and flies up as high as possible tossing the bomb away where it detonates safely, causing no harm to anyone. While the Russian military officials decide if they should re-imprison the X-Men or not, the three mutant heroes flee the scene.
The two teams of X-Men begin tracking the location of Factor Three. At the terrorist organization’s secret Midwestern hideout, the Mutant Master curses the X-Men for their victory, and begins to wonder where Changeling had gone, however he dismisses his second in command’s absence, and focuses on destroying the X-Men when they arrive.
The first to arrive are Cyclops and Iceman who are confronted by Vanisher, Unus, Mastermind and Blob. However they are only briefly outnumbered when Angel, Marvel Girl and Beast arrive on the scene shortly after. Before the two factions can begin fighting, Professor Xavier, recently freed tries to explain to the other Factor Three conspirators that Mutant Master has betrayed them by keeping the X-Men alive (by using the oblivo-ray instead of outright killing them and leaving the flying saucers to allow them to escape their European base before it self-destructed.) Realizing that Xavier is getting close to the truth behind his intentions, the Mutant Master then orders his androids to attack everyone, including his fellow Factor Three conspirators.
Elsewhere in the complex, Banshee revives finding that he too has been freed by parties unknown. Banshee then joins the battle and uses his sonic scream against Mutant Master, seemingly destroying his body. However, it turns out that his humanoid form was merely a disguise, and that Mutant Master is really an alien from another world. Claiming that it's from the planet Sirius. As it is battered by both Banshee and Unus, the creature explains it was attempting to exploit mutants in a bid to take over the Earth for its masters. Unwilling to accept defeat, the alien Mutant Master instead chooses death. During the course of the final battle, another Charles Xavier appears, and as it turns out the "Charles" who warned Factor Three and the X-Men about Mutant Master's hidden motives was Changeling, who was revealed to be a shape shifter.
With Mutant Master dead and his plot to take over the Earth ended, the remaining members of Factor Three and the X-Men agree to part company. Just as they escape in the remaining saucer crafts, the Professor tells Cyclops this cooperation between mutants against a common foe gives hope for the future.
Returning to the X-Mansion, Jean is excited to find that a package had been delivered in their absence, new costumes that she designed, and with Xavier's blessing, the X-Men dawn their new uniforms. The entire team is happy with their new duds, except for the Beast who is less than enthusiastic about the new outfit, Angel quips about how they could have made him a costume more fitting to his name, complete with fur and tail, everyone but Hank himself get a good laugh out of the joke.