X-Men Mutant Empire Series by Christopher Golden

They live as outcasts, hated and feared by the very humanity they protect. They are mutants born with strange and wonderful powers that set them apart from the rest of the human race. Under the tutelage of Professor Charles Xavier, they are more than mutants. They are the X-Men.

The Big Apple has been taken over by the X-Men's arch-enemy, Magneto. He's declared it a haven to all mutants, vowing to rule the new empire with his Acolytes--with their law enforced by reprogrammed Sentinels. The X-Men must penetrate the enslaved city and stop Magneto before he advances his mad plan to expand his empire from New York to the entire world!

Facing the loss of half their comrades with Magneto's latest successes in his creation of the Mutant Empire, the remaining X-Men are forced to team up with the U.S. government in an effort to reprogram the Sentinels.