Doctor Doom has used the Summers Rebellion to recover Cortex, an example of his 'Doomlock' technology. This technology allowed Cortex to shape the present (80 years hence) by travelling back to the modern era and murdering the ancestors of mutants without creating alternate timelines. And now that he's recovered Cortex, Doom orders him to dispatch all of the mutants present.

But the mutants have an even larger problem. Anthony Falcone, the scientist who was behind the President's anti-mutant measures, has traced Cortex back to the mutant's headquarters in Atlantic City. And now he's sending a massive force of sentinels to wipe them out.