Mr. Sinister send Mystique to destroy the X-Men while Professor X is lost in the Savage Land. Rogue starts having painful visions of a mysterious woman and they're literally driving her crazy when the mysterious woman possesses Rogue's body. Unknown to the X-men, this mystery woman holds some dark secrets to Rogue's past before she joined the X-Men.
The Friends Of Humanity attack a hospital for the blind that Beast is working at. And Wolverine plans on tearing them apart from the inside. Beast and one of his blind patients, Carly, fall in love together. But Carly's father is a mutant hater and won't stand to see them associating with each other. When the Friends Of Humanity kidnap Carly for associating with a mutant, Wolverine, Beast, and the FOH come full circle. Meanwhile, in the Savage Land, Xavier and Magneto are struggling to survive.
On a world ruled by Television, an alien named Mojo is master. When he abducts the X-Men and forces them to be action heroes in his shows, he may have to deal with more than he bargained for when Mojo's original action hero sabotages him. Xavier and Magneto are still slowly making their way through the Savage Land.
Xavier and Magneto finally make their way back to Xavier's plane, only to be ambushed by some mutates. The new ruler of the Savage Land is revealed but not until they make a new ally. Morph sends a message to the X-Men revealing his location which provides an encounter with Mr. Sinister and his group of Nasty Boys.
The X-Men are now in the Savage Land and are powerless like Xavier and Magneto, which leaves the X-Men open to being experimented on by Mr. Sinister. The only ones left to rescue them are Ka-Zar and Wolverine. Once everyone regains their powers, the Savage Land is restored. But what does the future hold for the Savage Land now?
Wolverine is lured into the Morlock tunnels by a former lover who is accompanied by a group of cybernetic mercenaries called Reavers. Wolverine discovers this woman he used to love isn't the woman he once knew, as she's gone through the same cybernetic alterations that the Reavers have, and a new moniker, calling herself Lady Deathstrike. She has discovered a long buried alien craft and needs Wolverine's adamantium claws to cut it open.
After being released from an alien spacecraft, a being called the Spirit Drinker starts draining the life force of the people around it, including The Reavers, Lady Deathstrike and Jubilee. Can the X-Men figure out the secret of destroying it before the drained life forces are gone forever?
Professor X's visions leads to his decision to blindly send the team to commandeer a space shuttle on which they are then attacked by Shi'ar agent Erik The Red who has plans to ambush the rebel, Lilandra when she exits a space wormhole. Jean Grey experiences a transformation as the shuttle travels through an energy field.
A psychic probe in the form of a beam of light causes Professor X's to emit a psychic projection of his dark side which then attacks the X-Men. Professor X retreats to Muir Island for rehabilitation but is visited by Lilandra.
Juggernaut and Black Tom Cassidy kidnap Lilandra for Erik The Red but the X-Men track them down. A fight results in a stalemate until Gladiator, guard to the imperial throne, shows up to take Lilandra captive. Phoenix rescues her and vanquishes Gladiator for the meantime.
The X-Men fail to protect the M'Kraan Crystal from intergalactic pirates called Starjammers who plan to sell it to D'Ken as well as to use Cyclops as an assassin. Phoenix transports the X-Men to the crystal but D'Ken succeeds in unlocking it's power.