Since the dawn of civilization, he was worshipped as a God. Apocalypse, the first and most powerful mutant from Marvel's X-Men universe, amassed the powers of many other mutants, becoming immortal and invincible. Upon awakening after thousands of years, he is disillusioned with the world as he finds it and recruits a team of powerful mutants, including a disheartened Magneto, to cleanse mankind and create a new world order, over which he will reign. As the fate of the Earth hangs in the balance, Raven with the help of Professor X must lead a team of young X-Men to stop their greatest nemesis and save mankind from complete destruction.

Sentinels, robots that were created for the purpose of hunting down mutants were released in 1973. 50 years later the Sentinels would also hunt humans who aid mutants. Charles Xavier and his X-Men try their best to deal with the Sentinels but they are able to adapt and deal with all mutant abilities. Charles decides to go back in time and change things. He asks Kitty Pryde who can send a person's consciousness into the person's past to send him but she can only send someone back a few weeks because if she sends someone back further it could harm them. So Logan decides to go back himself because he might be able to withstand it. So Charles tells him that it's Mystique who's responsible because when she learned about the Sentinels she sought out Bolivar Trask the man who created them and killed him. She would be caught and studied and her ability to change was somehow added to the Sentinels which is why they can adapt. Logan must go to the younger Charles and ask him to help; problem is...

Before Charles Xavier and Erik Lensherr took the names Professor X and Magneto, they were two young men discovering their powers for the first time. Before they were archenemies, they were closest of friends, working together, with other Mutants (some familiar, some new), to stop the greatest threat the world has ever known. In the process, a rift between them opened, which began the eternal war between Magneto's Brotherhood and Professor X's X-MEN.