In the year 3999 A.D., Cable and the rebel forces are seen fighting against Apocalypse and his army of machines. Suddenly a temporal storm appears. After a consultation with his computer, Cable finds out that the temporal storm is realigning his timesteam, effectively destroying it as changes in the past have led to the non-existence of his current time.
Bishop returns from the past after successfully stopping the assassination of Senator Kelly. To his dismay, he finds that a new problem has arisen and there is still conflict during his time. Mutants are now afflicted with a deadly virus, and the X-Men appears to have died from the virus as well before they can stop it. Bishop has Forge send him back to the 21st century to stop the plague.
Jubilee and Storm are at the mall to get Jubilee’s broken CD player fixed. Storm browses the bookstore while Jubilee gets her player fixed. Creed, leader of the Friends of Humanity, seizes the chance to set Jubilee up so mutants will get blamed for carrying and spreading the plague. Jubilee gets chased by an angry mob. Storm comes to her rescue and they make their way back to the mansion.
Beast and Jean have Jubilee checked out for any signs of illness. Jubilee is given a clean bill of health. Beast grows curious about the virus. He sneaks into the hospital where the infected man was warded to learn more about the virus. Meanwhile, the city has called to quarantine mutant safehouses.
Bishop tries to stop a riot outside a mutant safehouse. He is joined by the X-Men. After dispersing the crowd, the X-Men are quick to assume that the presence of Bishop means trouble is brewing nearby.
Back at the mansion, Bishop relates his new findings of the future. The X-Men have likely died of the virus early on, a virus that was engineered in a lab. Beast backs up Bishop’s statement with his own research into the virus. The X-Men contact President Kelly, who has invited Beast to join the hearings of the Senate regarding the virus.
At the headquarters of the Friends of Humanity, Creed is pleased that his scheme is panning out nicely. He plans to use Beast as a scapegoat at the Senate hearings. Unknown to him, his lead scientist is Apocalypse in disguise, with a virus created to rid the world of “mutants and humans”.