Stryfe, with Cable's visage, attempts to assassinate Professor Charles Xavier during a speech on equality by shooting him in the head with a techno-organic virus slug. Xavier's body is soon overrun by a virus that turns each infected cell into a technological circuit. Beast and Moira MacTaggert work tirelessly on restoring the professor but to little avail.
As the Professor is being attacked, Cyclops and Jean Grey eat at Harry's Hideaway, during which Caliban barges in and kidnaps the two. Colossus and Iceman try to help but they are attacked by two more of the Horsemen of Apocalypse. The foes are defeated and it seems that Apocalypse is behind the schemes to kidnap the two X-Men and kill the Professor. Yet, once Cyclops and Jean Grey are handed over, it seems as if Mr. Sinister is orchestrating the events. Apocalypse is actually awakened during a regenerative sleep to be informed that actions are being done in his name.
Meanwhile, X-Factor seeks out the attacker with a few select members of the X-Men. X-Force, not wanting to believe their mentor could be behind such a thing, sets out in search of the real assassin. They run in to the other X-Teams and try to fight their way out. X-Force is soon apprehended and held captive in the Danger Room. Mr. Sinister shows up at the X-Mansion and tells that Stryfe is really behind it all.
Cable shows up and learns about the current events. Believing Canadian intelligence has the answers, Cable arrives in time be confronted by Wolverine and Bishop, two guys who had the same ideas about the Canadian intelligence, but for information on Cable's safehouses. A fight ensues and Cable talks the two others into believing that he is innocent. The three then escape the government building and teleport to Graymalkin, Cable's space base, where Cable explains that he and Stryfe are both from the future and share a face. There, Wolverine receives a signal from Jean and the three men figure out the location that Cyclops and Jean are being held.
Apocalypse breaks into one of Cable's safehouses and starts to piece together that Cable or Stryfe is the son of Cyclops. He then returns to Egypt. His Dark Riders are easily defeated by Stryfe. Stryfe then turns his attention to Apocalypse and nearly kills him. Apocalypse is able to teleport away before the death blow.
During the events, Stryfe has tortured and tormented Cyclops and Jean, accompanied by parental taunts. The two are finally able to escape only to find they are being held captive on the Moon.
On earth, the Beast is able to remove the techno slug, but the Professor's condition doesn't get any better. Fortunately, Apocalypse shows up and convinces the X-Men to let him help cure the Professor. After all, he did use the same stuff to form Archangel's wings, as well as infect the son of Cyclops in the Endgame story arc. The team reluctantly agrees and Apocalypse (after regenerating) cures the Professor by accelerating the infection. With the virus out, the Professor sleeps deeply. The remaining members of the X-Men, Apocalypse included, head to the Moon.
Cable, Bishop and Wolverine are already on the Moon and under heavy attack. The X-Teams show up in time to help defeat the Dark Riders. The teams then spread out to find Cyclops and Jean, as well as Stryfe. Stryfe, meanwhile, has recaptured Cyclops and Jean and removed them to different location. Cable, Havok, Polaris, and Cannonball track Stryfe to a building but a gray force field only lets those in of Summers blood. Cable then fights Stryfe. Losing, Cable is able to find relief from Havok, who made it through. With the assault on Stryfe, Cyclops and Jean are able to break free of Stryfe's hold and help in the fight. Cable knows the only way to finish the fight is to take Stryfe out for good, which means taking himself out, too. Cyclops triggers the mechanism that opens a portal into which Stryfe and Cable are pulled to their supposed deaths. Cyclops doesn't know for sure, but he can't help but feel as if he's let his son go again.
Mr. Sinister is finally seen to open a canister, his payment for the part he played in Stryfe's game. Instead of the promised genetic make-up of the Summers family, the canister is supposedly empty.
Xavier could walk again, albeit briefly, due to the effects of the techno-organic virus. Rogue was blinded by the MLF member Strobe. The effects would only last a few weeks, but that time was spent mostly around Gambit.
Cannonball stepped up and took the reigns of leadership of the team.
Mutant Liberation Front
Each mutant member not killed is arrested (except Zero). Only some are released when Reignfire later restarts the MLF.
Cable and Stryfe
Both men were seemingly lost into the vortex. Cable later returns, but Stryfe's mind is locked into Cable's brain. He resurfaces at later times but is always defeated.
Mutants in General
The canister Mr. Sinister opened wasn't empty. It actually contained the Legacy Virus, a disease that largely only affected mutants.