X-Factor and the freed X-Men battle the controlled X-Men and Muir Islanders, and the Shadow King is eventually defeated when a Forge frees Psylocke, who plunges her psychic blade into Polaris's head and disrupts the Shadow King's link to the physical world.
The series had several lasting results for the X-Men family of characters:
Muir Island was destroyed and the Muir Islanders disbanded.
Polaris lost her super-strength powers but regained her magnetic powers.
Xavier was forced back into his wheelchair.
Muir Island Saga Event: Episodes and Synopses
Pt. 1 - The Battle of Muir Island
The battle begins...
Pt. 2 - Bad to the Bone
Under the mental control of the Shadow King, Colossus chases Xavier and Stevie Hunter through the ruins of the Xavier Institute. It comes to a showdown between Xavier and the Shadow King in the Danger Room, and Xavier realizes that he can only free Colossus by destroying the artist Peter Nicholas personality in Colossus head; though it hurts him as Piotr actually was happy as an artist. On Muir Island, only Forge remained free from the Shadow King’s influence and the other X-Men are hunting him. Yet Forge is able to use a neurosynaptic scrambler on Wolverine and when being discovered by Rogue, he knocks her unconscious with a gun. The Shadow King realizes that he needs a new host body, as that of FBI agent Jacob Reisz is beginning to deteriorate. Xavier, Stevie and Colossus witness a riot in Salem Center which is actually the Shadow King’s doing, they decide to call in X-Factor.
Pt. 3 - Clash Reunion
On Muir Island the Shadow King has taken over the minds of the most X-Men. Forge was able to design a device that frees him from the mental hold, and he is able to use it on Rogue, Wolverine and Banshee too. Sean knows the extent of the Shadow King’s plan. He psionically causes world wide waves of hatred and prejudice, that will bundle in the form of Lorna Dane. Being a catalyst for negative emotions, she has been made his nexus between the physical and the astral plane, and he is getting stronger by the minute. In Washington, Val Cooper and Xavier call in X-Factor for a rescue mission. They secretly approach Muir in a submarine, but aboard is also FBI agent Reisz, the Shadow King’s human host. When X-Factor invades the island, they are held in check by Legion, under the King’s control. On the submarine, Reisz starts to strangle Xavier, who pleads Val Cooper to help, yet she is under the King’s control too – or so he thought. She suddenly shape-shifts, revealing to be the believed killed Mystique and shoots Reisz trapping the Shadow King on the astral plane. X-Factor and X-Men wonder how to free Lorna Dane from the nexus gate to prevent the Shadow King from acquiring a new host. Caught in the dilemma that separating Lorna from the device might kill her, they hesitate too long and the Shadow King takes over Legion as his next host.
Pt. 4 - One Step Back--Two Steps Forward
Xavier inspects the ruins of Muir Island and finds X-Factor and the free X-Men held in a telekinetic field by Legion, who has been made the Shadow King’s new host body. The Professor and the Shadow King fight while Storm, who had remained hidden after her defeat by Legion, zaps him with lightning, causing him to loose control over the telekinetic field and retreat. Xavier and the free mutants come up with a plan, Xavier will engage the Shadow King on the astral plane, with Jean anchoring him and Storm, Cyclops, Colossus and Archangel shielding them from physical attacks, while Beast, Banshee, Iceman, Forge and Rogue will enter the lab complex to disrupt the Shadow King’s nexus. Xavier is not faring very well on the astral plane, as his astral injuries all show on his physical body too. First his legs are broken and he suffers more injuries. The lab team has to fight the mutants still influenced by the Shadow King, and many personal issues hinder them, like Banshee having to go up against Moira and Siryn for example. The team that is supposed to guard Xavier enters the astral plane too through Jean’s telepathy to help the Professor, yet this exposes him to physical danger in the form of Legion lurking around. The Shadow King now can destroy both Xavier’s mind and body, but before he fulfills his deed, Forge uses a neurosynaptic weapon on Psylocke and while she is still dazed, he plunges her psychic blade into Polaris’s head, disrupting the Nexus and the Shadow King’s power source. The Shadow King vanishes, Legion falls unconscious and Xavier’s back is broken, but the X-Men won and the dream is still alive.
Pt. 5 - Ends and Odds
After the fight with the Shadow King, Legion is in a coma and Xavier tries to wake him up. After many mental probes Xavier accepts that he is unable to help his son. He returns from the astral plane to his physical body and is informed that his legs have been crushed, meaning he again will be confined to a wheelchair. With the original five X-Men returning, the X-Men now have fourteen members. Mystique and Val Cooper explains how Mystique was not killed, but only replaced Val to fool the Shadow King. Mystique and Rogue reunite. Val thinks about restarting a governmental sanctioned team and offers Polaris, Multiple Man and Guido to join.