While in Korea during the war, Charles Xavier and his step-brother Cain Marko stumble into a cave. In the regular 616 universe Cain finds the gem which turns him into the Juggernaut, in this story Charles finds it first. The cave is destroyed, while Cain escapes while Xavier is buried under the rock.
Sometime passes and Magneto leads an army of Mutants against the world. When they are about to be defeated, Xavier appears as the Juggernaut and using both his mental and physical powers is able to lead the mutants to victory. Magneto, being replaced as leader, disappears.
Years pass and the USA (or perhaps just New York) is a mutant ruled slum where normal humans are abused by their mutant 'betters'.
Cyclops is a member of the elite, alongside his wife, Jean Grey. They both have become disillusioned with Xaviers rule and the oppression. They gather their mutant comrades together and ask for anyone to join them in seeking to change their world for the better. Only Quicksilver and the Scarlet Witch join them.
They are then approached by Cain Marko who offers to put them in touch with the one man who may help them, Magneto.