It has been month's since the fateful day the X-Men took a stand against Magneto's army on the island of Alcatraz. Since then, Jean has returned as well as Scott Summers and Professor Charles Xavier each in their own ways, intent on continuing the guardianship that is the X-Men. Headmistress Ororo Munroe now operates most of the X-men alongside the mentor Charles Xavier, together they work diligently to strengthen the team for war.
But, as new students pour in, danger brews much darker than Magneto's plotting or the Phoenix's rage. His name is En Sabah Nur, and he is an ancient Egyptian mutant that now calls himself the "Apocalypse." Apocalypse is gathering his plans behind the veiled eyes of every man, woman, and child. Gathering his four Horsemen, he plans to spread his great power over the Earth, awaking the X-Gene in every human and furthering the mutant abilities in the already mutated others. It would settle the feuding civil war between the humans and the mutants as the Government wishes to enslave every mutant under Rights Acts and ordering them to Register their name and powers to the National Database. With such a thing in force, the government could know everything and everyone when the time comes to take drastic steps.
Madelyne Pryor, the clone engineered by Mr. Sinister has been chosen as War, the first of the four Horsemen, ready to carry out Apocalypse's plans. She now brews trouble with secret spies in the ranks of the X-Mansion, gathering the evils of all to find the other three horsemen and begin the End.
Meanwhile, the ranks of men have been gathering their own forces against the oncoming war. Intelligent robotic creatures named "Sentinels" have been given life by the Secretary of State, Bolivar Trask, who's interests in the fire power against their enemy has formed this malicious creature. The Sentinels are created with the highest levels of intelligence and weaponry. They are designed especially to take out mutants but their modifications of late have been to cooperate with aiding mutants, such as the X-men. But these creations are also given one powerful and determined objective: to bomb the greater part of the North American Apocalypse Forces. If this were to happen, anyone, human or mutant, would be caught in the crossfire and utterly destroyed on contact.
Forces of all kinds gather together to band against the greatest power of all evils. X-Men and mutant affiliates from their own futures visit the X-men to join their gifts for all the help they can get. Magneto bands his Brotherhood of mutants to Xavier's X-men in hopes that an alliance is the best way to stop this threat. Magneto goes so far as to become a teacher at the Mansion, aiding the children with his own great intellect.
Which side do you fight for? Do you take side with the heroic X-Men, forever fighting for the rights of man though the humans stab them in the back? Or understand and agree with the Apocalypse's visions for the all-mutant future?