Published between 1996 and 1997, Christopher Golden wrote three X-Men novels collectively known as the Mutant Empire Trilogy. Individually, they were known as X-Men: Siege, X-Men: Sanctuary, and X-Men: Salvation.
The novels focus on two plots concurrently: the main plot centers around Magneto and his Acolytes hijacking a fleet of Sentinels and using it to seize control of Manhattan, while the secondary plot focuses on a secondary squad of X-Men led by Cyclops and Jean Grey in space battling the Shi'ar Empire. They take place in the mainstream Marvel universe, and though published in the late '90s they are set in the early '90s era of that universe, just prior to Fatal Attractions (Marvel Comics).