New York in 3999 AD is a wasteland. Buildings are decrepit or destroyed. The Apocalypse has come and rules. Nevertheless, wherever there is tyranny, there is a resistance. Cable rallies his troops once more against Apocalypse’s metallic infantry with a cry of “victory or death.” Apocalypse watches on unmoved. He is eternal –impervious to mere mortals’ machinations.

Then the unexpected interferes. A temporal storm materializes in the battlefield destroying Cable and Apocalypse’s forces alike. Cable’s entire troupe disappears, and he flees. He demands his portable computer explain what is occurring. The computer passively replies that the past has been changed and the time stream is realigning –destroying Cable’s world.

Cable asks another question. What has changed? The computer explains that the past was altered by a time traveler from the 21st century named Bishop.

New York in 2055 AD is a wasteland. The buildings stand but a plague ravages the population-killing mutant and human alike. The newly returned Bishop knows nothing of the plague since he was in the 20th century, a temporal anomaly.

Forge explains that after Senator Kelly was elected president he dedicated his term to mutant rights, and there was a backlash from mutant-haters. The backlash spawned a genetically constructed disease. The disease became an epidemic. Apparently, the virus was not fatal until it combined with mutant DNA.

Bishop asks, “Couldn’t the X-Men find a way to stop it?” Nevertheless, the timeline has altered so radically that Forge does not even recognize the name of the group. Bishop demands the opportunity to alter this timeline as he did before.

Present day New York is a wasteland. Crime thrives, poverty increases, a new virus that has everyone scared. Bishop lands in the same abandoned alley as before. He buys a newspaper and reads the plague has already begun. He rushes off to the X-Men’s residence.

Meanwhile Storm and Jubilee are at the mall –Storm to buy books; Jubilee to get her walkman fixed… again. On the way into the electronics store, a Friends of Humanity goon recognizes Jubilee and trails her. The clerk at the store takes Jubilee’s walkman into the back and tries to fix it. The FoH henchman pokes his head into the room silently, fires a viral weapon, and departs. The repairperson skin flushes and begins to sweat.

The clerk returns Jubilee’s walkman unfixed and collapses. He has been infected, the Friend of Humanity member emerges from the onlookers and loudly proclaims Jubilee to be a “plague-carrying mutant.” The crowd is about to turn on her when Storm conjures a fog so they may escape.

At the Westchester Mansion, Beast gives Jubilee a check-up. She is healthy (except for some vitamin deficiencies that stem from her not eating enough vegetables.) Beast decides that only scientific inquiry can cure the plague, and a little research may be necessary. Later Beast sneaks into the hospital and procures the store clerk’s file.

Back at the mansion, Cyclops calls a team meeting. Rogue, Storm, Jean, Gambit, and Wolverine all assemble. They watch as city officials begin quarantining a mutant’s home. A crowd has amassed outside among them is the same FoH crony that was at the mall. Storm recognizes him. Cyclops suggests the X-Men should intervene before the mob gets unruly.

Bishop stumbles upon the mob first. When members of the FoH attack him, he strikes back –exacerbating the situation. When the X-Men arrive, they now must calm the mob and Bishop. Fortunately, when Storm conjures a thunderstorm most of the mob disperses. One straggler fires a plasma rifle at Storm and hurts her. Rogue disarms the hoodlum and tosses him in a garbage can.

Cyclops berates Bishop for his hot temper. Bishop retorts, “I was trying to save lives, yours and millions in my future.”

“Again?” Wolverine quips.

The X-Men return to the mansion, and Bishop explains the stakes. This artificial virus is about to turn deadly, and it will run rampant over the western world. Beast corroborates Bishop’s assertions with his own evidence accumulated from the hospital records.

At the FoH headquarters, Graydon Creed compliments a scientist on his well-designed plague. Creed suggests that he infect Henry McCoy when he testifies in front of the Senate Hearing Committee. The scientist humbly agrees. After Creed leaves the room, the scientist grins sinisterly. He laughs to himself, and his laugh is the laugh of Apocalypse.

The next day Creed testifies in front of the committee. The committee is skeptical toward Creed’s allegations, but he obviously has public support. When Creed finishes his rant, it is McCoy’s turn to speak. As Beast approaches the podium, Creed pulls a small weapon from his suit pocket. Bishop sees the weapon and tackles Creed. During the ensuing melee, Creed falls ill and blames Bishop. Worse, it is all televised nationally.
In the Blackbird Beast reviews the tape of his assault and sees Bishop was right. Creed infected himself on accident with his own viral weapon. Cyclops decides to trail Creed to his headquarters.

Back in 3999 AD, Cable demands to know who Creed is. The computer replies, “The mutant named Bishop remains the key.”

The X-Men infiltrate the FoH’s headquarters by force. After summarily dispatching the FoH thugs outside, the X-Men and Bishop descend to the basement’s secret laboratory. The scientist that Creed spoke to earlier is furious with Graydon for leading the X-Men there, so furious he reveals his true self.

The X-Men and Bishop try to injure Apocalypse by force, but Apocalypse just chuckles condescendingly and again declares himself “eternal.” Creed faints. The battle goes badly for the X-Men. They are out-powered. Then, Bishop tricks Apocalypse into destroying his own lab and beloved plague.

The X-Men flee as the lab explodes. Beast benevolently carries Creed outside, but Apocalypse is enraged. He grows to gigantic proportions and fires on the X-Men.

Cable cries out in anguish as he realizes his task. To save his world, he must help Apocalypse destroy a past one.