The Starjammers and X-Men are repairing damage to the Starjammer, using their powers from outside the hull to effect repairs. Cyclops and Mam'selle Hepzibah rescue Wolverine from being set adrift by a freak explosion that throws him free of the ship, but in the excitement no one notices Colossus collapse until after Wolverine has been rescued. Colossus is returned to Sikorsky's care.
Inside the vessel, Lilandra tries to communicate with Chancellor Araki, but receives no reply. Replying would be hard given that Admiral Lord Samedar has just shot him to death! Before Lilandra attempts to contact anyone else, Samedar orders communication frequencies jammed, leaving the Starjammer incapable of communicating the Empress's safety. Xavier suggests he could establish telepathic communication, but while concentrating he discovers an alien presence within him. He tries to probe it, but this merely causes him to call out in agony, and he collapses into a coma!
Inside the wounded Acanti, Deathbird is assaulted by the Brood in revenge for the damage that she has brought upon them by the debacle Lilandra's kidnapping became. However, they had not figured on how great a fighter Deathbird is, and so at last a truce is reached. Deathbird convinces the clan-master that the X-Men are worth the price, if they can be captured, for they will make exceptional hosts for Brood larvae. While cooperation seems assured once again, Deathbird plans treachery.
On the Shi'ar flagship, Kitty and Nightcrawler notice the ship being called to battlestations. Using the clothing generator to make her a short-term spacesuit, Kitty phases out through the outer wall (the only wall she can phase through of their room) and walks over to an airlock where she phases back into the ship. She makes her way through the corridors back to the door of their compartment to let Nightcrawler out, only to see assassins assembling outside. She phases through them as they open the door to warn Nightcrawler, shorting out their armor, and the two X-Men make short work of the Shi'ar soldiers. They go to Araki's quarters where they discover Araki's body. Quickly they hatch a plan - they need to distract the Shi'ar to delay the firing and capture Oracle, a telepath who can read their minds to ascertain the truth.
On the bridge the Imperial Guard is questioning Samedar's order to conduct punitive bombardment of Earth. Just then, Nightcrawler rapidly teleports through the bridge, filling the room with smoke. Under this cover, Kitty phases up through the floor dressed as Phoenix, and as the smoke clears threatens the Shi'ar with dire consequences should they attack her 'home'. Nightcrawler then teleports to Oracle and away with her quickly, making it look like she just disappeared. Disoriented from porting, Oracle still believes Kitty is the real Phoenix, and tries to run. Eventually the X-Men convince her of the veracity of their tale, and summons Gladiator. Oracle convinces Gladiator, but Gladiator is worried about some of the Imperial Guard who might side with Samedar.
Those same Imperial Guard break through the wall just then, ending any doubts whose side they are on, and battle is joined. Kitty starts out helping, but Kurt orders her to disable the ships computers, so down through the floor and towards the core she phases. However, before Kitty can get the secondary core she is neutralized by a defensive weapon, and our heroes in the melee are similarly defeated by a Brood weapon secreted on one of the traitor Imperial Guard. His ship finally returned to Samedar's total control, the Admiral orders the main weapons batteries to open fire, but the Starjammer emerges from hyperspace just then to block the shot! Lilandra broadcasts to all vessels that she is safe, and the danger to Earth is over.
At the end we learn that Colossus is recovered, although he would still benefit from rest. But Professor X has not stirred...