Taking place immediately after the events of the 1990 crossover "Days of Future Present", a group of Genoshan Magistrates (soldiers of the country of Genosha), backed by the cyborg Cameron Hodge, and including an amnesiac Havok (a member of the X-Men), attack the X-Mansion and kidnap Storm and the New Mutants Warlock, Boom-Boom, Rictor, and Wolfsbane. Warlock is killed and Storm and Wolfsbane are brainwashed, turned into mindless mutate slaves, which form the backbone of the Genoshan economy and lifestyle. Cable, the New Mutants, Gambit, Forge, and Banshee recruit X-Factor and head to Genosha to save their teammates. They are soon joined by Wolverine, Psylocke, and Jubilee, who independently head to Genosha to rescue their friends.
In the end, the X-Men defeat the forces of Genosha and Cameron Hodge's severed head is buried alive by Rictor, who uses his earthquake-inducing powers to topple the Genoshan capital building "The Citadel" onto Hodge. Storm, whose body had been physically regressed into that of a child in an earlier story, albeit with her adult memories and personality intact, was freed of the brainwashing, and regained her adult form. Wolfsbane was also freed from her brainwashing, but was trapped in a lupine form permanently. Havok (having gotten his memories back) elected to stay in Genosha along with Wolfsbane to help rebuild the now anarchic country and keep it from civil war between its human and mutant population.
Storm is examined by Forge, but her condition of being stuck in a child’s body seems to be permanent. She renews her deep friendship with Jean Grey who visits from X-Factor. Later the school is attacked by Genoshan troops and surprisingly the missing Havok is with them. Storm realizes that they are outnumbered and taken by surprise and so she decides to lock the underground complex. By this she dooms the fates of herself, Boom-Boom, Rictor, Wolfsbane and Warlock who are all captured and teleported to Genosha, but she ensures that at least the other halves of the teams remain free to prepare a rescue mission. In Malibu, Lila Cheney teleports back from outer space and mentions that Xavier is in terrible danger before passing out.
Storm, Boom-Boom, Rictor, Wolfsbane and Warlock have been captured by Magistrates and teleported to Genosha, where they learn that Cameron Hodge, now using a huge mechanical body, has allied with the island nation. The mutants are stripped of their powers and prepared for undergoing the mutate process, but Warlock sacrifices his last energies to help his friends to break out. They split up and try to escape the citadel, but Rahne later turns back to help Warlock. She arrives just in time to prevent Hodge from infusing himself with Warlock’s shapeshifting ability, but she can’t prevent her teammate’s death. In New York, X-Factor and the remaining New Mutants and X-Men learn of their friends whereabouts through the TV news. Genosha considers the X-Men as criminals of the state which will be brought to trial, Warlock is reported to have been killed while trying to escape.
The Genegineer and Cameron Hodge don’t go along well, but Genosha's President Madame Reneau reminds Moreau that they need their insane ally for a while longer. While the US government officially does not get involved, they unofficially support a rescue mission of X-Factor and the remaining members of New Mutants and X-Men. Once on the island they get attacked by a Magistrate strike force under Havok’s command, but despite the surprise of seeing their former member Havok with them, they can fight them off. Boom-Boom and Rictor escape the citadel, while Storm plans to take someone hostage.
Jubilee, Rictor and Boom-Boom manage to elude the many Magistrate patrols in Hammer Bay’s streets. Cameron Hodge and the Genegineer transform Wolfsbane into Mutate 490. Half of the rescue team (Cable, Gambit, Marvel Girl, Sunspot, Forge) try to plant explosive devices around the citadel but are discovered and kept busy in battle till Wipeout negates all their powers. Having heard the news of Rahne's mutate bonding process, Tabitha, Ric and Jubilation also planned to attack the citadel, but they arrive just in time to witness the fate of Jean’s team. Helplessly they watch from a safe distance, but at least the can avoid re-capture.
Cameron Hodge examines his recent captives (Marvel Girl, Cable, Gambit, Sunspot and Forge) and is angry that the inventor Forge is in an unexplainable coma for he wanted to utilize his cybernetic knowledge. Jean is brought into a prison cell, where she meets the dying Wolverine and shares a moment of passion with him. Cyclops, Iceman and Beast infiltrate the citadel disguised as mutates while Banshee, Cannonball and Archangel cause a distraction at the citadel’s penthouse. Soon the flight team is defeated by Hodge and the others are exposed too. Hank and Bobby get trapped between sliding walls, while Cyclops is forced to fight Havok. Right as Alex remembers his past life as an X-Man Cameron Hodge arrives and captures Cyclops. Havok decides to pretend to be the still loyal Magistrate, and plans to attack when least expected.
The captured members of the X-teams are put on trial in Genosha. They are offered to volunteer for the mutate bonding process, otherwise they have to face death. All of them choose the later and are brought to Cameron Hodge, who enjoys to have so many “toys“. The mechanical monster has Archangel and Wolverine fight each without restraints and forces the others to watch. Psylocke pretends to no longer bear the brutality and accepts to be transformed into a mutate. Soon after she is led away she surprises her guards with her Asian ninja skills and escapes. The Genegineer Moreau and Tam Anderson decide that Hodge has finally snapped and plot behind his back. Outside the citadel Dr. Moreau orders a mutate to create a tunnel below the citadel; not aware that they are being watched by Rictor, Jubilee and Boom-Boom. Cameron Hodge murders Wipeout and frames Magistrate Havok for the crime, getting rid of both the only way for the X-Men to regain their powers and a possible opponent. Tam Anderson and Psylocke take mutate 20 (Storm) to the prisoners, who have just freed themselves thanks to Gambit’s lockpicking. Something strange happens as Storm hits Cyclops with a lightning. Ororo is back to her former adult self and has washed off all effects of the mutate bonding process and Scott too has back his optic blast.
After Storm restores both Cyclops and Jean‘s powers the three together fight Cameron Hodge, but he is slowly winning; suddenly the citadel is shaken by a bomb explosion in the basement lab complex. While Hodge rushes away to safe all of his information stored there, Storm restores all the X-teams‘ powers as Cyclops reveals that the explosion was caused by a robot autobomb of Forge’s design. To ensure the secrecy of this back-up plan, Forge had willed himself into unconsciousness to avoid mindscans. The mutants split up into three squads, two try to battle Hodge, the third will search for Wolfsbane.
Downstairs Cameron Hodge checks the computer systems and find the mainframe still active, he leaves again to hunt the mutants by utilizing much of the computers sensory input like body heat signatures, and building blueprints.
Rictor, Tabitha and Jubilee followed the Genegineer through a secret tunnel into the basement lab complex where they discover Wipeout's dead body guarded by mutate 490 (Rahne). At first Ric and Boom-Boom believe the only way to restore their powers is gone, but then Storm, Cable and the other New Mutants arrive in the labs. With lightnings Ororo is able to reverse the power-negation, but Wolfsbane can only partially be restored. In wolf-form she has free will, but in human appearance she will be the mindless mutate again.
The mixed groups of X-Men, New Mutants and X-Factor members hunt their opponent through the citadel and run into various fights with the mechanical monster during which many receive major injuries, though Hodge too is weakened. During one of these battles Hodge snaps the Genegineer‘s neck.
As the X-Men watch, Cyclops and Havok do battle with Cameron Hodge. Despite their power, Hodge cannot be killed. Havok lets his guard down and is snagged by Hodge, who tries to pull the Summers brothers over the edge of the citadel. The three fall, but Jean is able to pull Hodge away and save the brothers. Knowing he'll just come back, Rictor drops the citadel on top of him, burying him alive.
In the aftermath of the battle, the military takes control of the government to prevent a human/mutant civil war with Havok and Wolfsbane staying behind. The New Mutants honor Warlock's last wishes and spread his ashes over Doug Ramsay's grave. That night, those ashes seem to sparkle...
Published during the comic book speculator boom, the involvement of Jim Lee and Rob Liefeld caused the issues of the crossover to sell for $10-20 on the secondary market when the books were first published, though the issues have since gone down in value.