The X-Men, Trish Tilby and Deathbird have teleported into the heart of the Shi’ar royal palace, where the Phalanx have taken over. Through a grating in the X-Men’s hiding place, they can see that the Phalanx have killed almost everyone in the palace except the Shi’Ar Majestrix Lilandra Neramani, Deathbird’s sister and consort to Professor X. Deathbird realizes they are torturing Lilandra to find out the location of the chamber where the Shi’ar keep their unhatched young. If the Phalanx were to find this place the entire next generation of Shi’Ar would be obliberated. Rogue, generally accepted as the leader of this team, sends Bishop and Deathbird to go to the hatching chamber, while Beast tries to discover a way to destroy the Phalanx.
On Earth, at the former Hulkbuster Base that is now the home of Bastion’s Operation: Zero Tolerance, Henry Peter Gyrich and Senator Robert Kelly oversee the activities. Kelly starts feeling doubts about Bastion’s operation, despite his own anti-mutant feelings.
In the Shi’ar palace, Bishop and Deathbird arrive at the hatching chamber which in Shi’Ar language is called “The Nest”. Bishop is amazed by the beauty of the place and it becomes apparent that some feelings are developing between them. Deathbird is still weak from her previous injuries, but she insists to help fighting the Phalanx.
Back with the others, Joseph looks at the many dead Shi’ar left from the Phalanx attack, and starts remembering scenes of the Holocaust. As his rage starts taking hold of him, Beast works on sending out a frequency that will separate the Techno and Organic parts of the Phalanx. Tormented by the Holocaust memories Joseph suddenly attacks, forcing Gambit and Rogue to follow suit. In the hatching chamber, Deathbird and Bishop are also battling Phalanx and it becomes painfully clear that they are completly outnumbered, but soon Beast’s plan works and all the Phalanx in the area are neutralized as all organic tissue melts from the technological components. The X-Men realize they have beaten the Phalanx, but not before thousands or more Shi’ar were massacred.