On a Shi'Ar Superdestroyer space ship, Cyclops and Xorn are held captive by the Imperial Superguardians. Both encased in restriction devices and held upside down, Xorn leans his head toward Cyclops and dryly asks if their situation is typical of life with the X-Men. Cyclops apologizes to Xorn, telling him that while he has no idea what hit them, they are currently on board a superdestroyer of the Shi'ar space empire. G-Type, the lead Guardsman on the deck, commands the two to silence. She then informs Cyclops and Xorn that she is to recite the Hymn of Purification prior to firing them into the Earth's atmosphere in a cremation ceremony.
Cyclops attempts to reason with G-Type, but Cassandra Nova, still in Xavier's body and surrounded with psychic energy, dismisses Cyclops as being insane. Cassandra, as Xavier, tells the mind-numbed Lilandra that all has been lost. He tells her that they must save what they can of the Institute's mutant gene-base and start again with clones on another world. Through the protestations of Cyclops, Cassandra/Xavier tells the superguardians that he and Lilandra barely survived the monster, Cassandra, in 4-space. "She" wrecked their craft and fled to Earth. Now, she says, the Imperial Superguardians can cleanse the planet of mutants. Controlled by Cassandra's telepathy, Lilandra tells Imperial Sage Araki to order the inhection team to kill them all.
Upon receiving authorization, Neosaurus leads four flying superguardians (Arc, Manta, Oracle, & Plutonia) over the Xavier Institute. Calling back the ship, he confirms the intelligence gathered by their primary scans. Oracle informs the group that there are telepathic sources all over the area; with a huge emission underground that she theorizes is Phoenix. Manta, using her ability to detect infrared heat sources, confirms the body count. Plutonia, after detecting an unusual alarm signal on the Imperial band, flies off to investigate.
Still in communication with the superdestroyer in orbit, Neosaurus questions why a team of superguardians is needed to take down a group of mutants when one superguardian alone could sterilize a city. Neosaurus gently floats to the ground, still complaining. After landing, Neosaurus points out that he has the most magnificent artificial brain in the galaxy, and that for once he would like to be treated with the respect that he deserves. A moment later, Wolverine bursts forth from some foliage and expertly removes Neosaurus' magnificent artificial brain with a single swipe of his claws.
Neosaurus' team, still nearby, have shackled Emma Frost and placed an inhibitor helmet on her head as they hear Neosaurus‘ death scream. One of the Stepford Cuckoos girls taunts the superguardians, telling them that the sound they heard is the noise Wolverine makes when he's chopping people into quivering lumps. Superguardian Stuff, back in his Kato guise, tells her to be quiet, and then informs the superdestroyer that he has seven mutants for sterilization. Another of the Stepford Cuckoos girls continues to chastise Esme, Kato's former girlfriend, for dating a "Prince Charming" that turned into an "ugly space frog". This statement draws the ire of Stuff, who tells the girls that he is glad that at least he is not stuck in one shape. Oracle, the supervisor of the prisoners, chastises Stuff for "morphism".
This distraction of attention by Oracle's telepathy gives the Stepford Cuckoos their opportunity. One of the girls tells Oracle that she should have been careful of distractions. While she has only one mind, they have five minds in one. As they speak, Oracle is drawn into a cloudy world of fear that exists within her own mind. Angel presses the surprise by knocking out Stuff with a right cross. Unconscious, Stuff reverts to his green one-eyed balloon form and floats helplessly before the girls. One of the Cuckoos, already sensing Angel's plan, tells Angel that if she runs away these horrible space people will kill everyone. Afterwards, she adds, they will come after her as well. The Stepford Cuckoos girl, not hearing any protestations, presses her plea and asks Angel if she has any idea how to fight super heroes. Cross-armed and angry at her situation, Angel says that she does: Dirty.
Through the halls of the Xavier Institute, Jean leads the dozens of invited reporters. Trying to concentrate on telepathically corralling the panicked media, Jean asks Beast to repeat what he has just said. Beast reiterates that they have been infected by Nano-Sentinels, which have been making them all more and more sick during the past few days. Jean tells Beast that if she looks hard and twisted enough, she can see how Cassandra planned the whole thing. Moments later, Jean, Beast and the group of reporters reach their destination: the vault. Jean opens the vault's massive door and explains to the reporters that they will be safe behind its ten feet thick walls. As a final thought, Jean places the students in charge of the people's safety and departs with Beast.
As they walk away, Beast points out to Jean that the ten feet thick walls will matter little to the Superguardians, who can punch through mountains and fly through steel. Jean asks Beast what they should do, Beast suggests self-destructing Cerebra if Cassandra makes it to them. Beast's next thought is interrupted by the Superguardian Monstra, who discovers their presence. Beast acts swiftly by raking Monstra's face with his powerful claws, effectively blinding her. The Guardian calls out to Fader, an unseen ally for help. Fader, hiding in the ultraviolet, fires his spazzgun at Beast but misses. Beast laughs at Fader, explaining that his hearing is ten times better than human and that his smell is the envy of aesthetes the world over. While Fader may be invisible to one of his sense, Beast assures Fader that the others are all over him. With this, Beast knocks out the unseen superguardian who slowly fades into sight.
Monstra, still blinded, calls Manta and Squorm for backup. Manta arrives first deftly avoiding Beast's claws as she flies over. Unfortunately, she is unable to avoid Jean, who manages to side kick her. After an elbow to the jaw and a wrist blow to the chin, Manta is down and out. By this time, Beast is under attack from a new Superguardian in bulbous armor, Squorm. Beast is able to tear apart Squorm's armor, effectively incapacitating him, but afterward falls to the electrical blasts of Arc, who has arrived with two more Superguardians. Through a window above, Wolverine bursts into the room. As he falls, Wolverine slashes Blimp, one of the two new Superguardians, with his claws. Blimp, who seemingly floats with an helium filled suit, starts venting his gas and begins to fly about the room uncontrollably.
To the Superguardians' surprise, Wolverine does not continue to fall, but floats in the air. Monstra announces to her comrades that Wolverine is employing an imperial flight patch, which has made him into an airborne foe. As the Superguardian calls her warning, Wolverine attacks the other floating Superguardian, who has split into two people. Turning a liability into an asset, Wolverine merely knocks their heads together, knocking them out. On the ground below, Arc activates his wrist communicator and calls Gladiator for assistance. Meanwhile, Beast, who has recovered from Arc's blast, uses the formerly helium filled Blimp as a bludgeon against Monstra. Next, Beast uses Blimp as insulator, wrapping him around Arc.
Beast has no time to revel in his victory as the wall begins to melt. Realizing his situation, Beast tells Wolverine that he believes that they are out of time. Through the hole he just created, Gladiator calmly strolls. He tells the X-Men that they have maimed Monstra and Blimp and have killed one of the exo-bodies of Neosaurus. This, he says, is proof of the sickness that Charles Xavier has described. Wolverine bears his claws at Gladiator and tells him to forget what Xavier has told him and think for himself. Gladiator ignores Wolverine's pleas. He tells the X-Man that he cannot help what the Cassandra Nova entity has done to him. Further, he tells Wolverine that as the infection is irreversible, he and his entire species must, unfortunately, be sterilized by imperial order.
Within the sealed vault, one of the reporters asks Jean what the noise he hears is. Another reporter asks for verification that Jean told them that the door had ten feet of steel. Realizing that nonetheless someone was coming through, he asks Jean if there is anyone that they can call. A white starry hand bursts through the door and opens a large hole. Through the hole Gladiator and another Superguardian enter. Both Superguardians drop Wolverine and Beast, whom they have been carrying. Wolverine, beaten and bloody, looks up at Jean and dryly tells her that he tried to talk them out of it.
Taking charge of the situation, Jean tries to reason with Gladiator. She tells the guardian that there is no psi-plague and that Charles Xavier's consciousness is trapped in the frail body behind her. Gladiator begins to counter Jean's argument, but is interrupted. He and everyone else turn to see Plutonia entering the room, carrying the half-dead Smasher. Plutonia tells Gladiator that she found Smasher, broken like glass and dying. Gladiator takes Smasher in his arms and listens to his weak words. Barely audible, Smasher tells Gladiator they have been betrayed. The monster lives within Xavier and has taken the mind of the Empress Lilandra. Jean nearly collapses in relief at their turn of fortune. Stoically, Gladiator looks upward and mutters that the empire has been polluted.
One of the reporters helps Jean back to her feet. She tells Beast that she feels like she's dying and asks what Cassandra has dosed them with. Beast, feeling the effects as well, tells them all that the have been dosed with tiny Sentinel machines developed in the Ecuador Master Mold. As Wolverine helps him up, Beast continues. He explains that bacterial robots were hiding in the blood Cassandra showered them with. Looking at his own hand, Beast mutters that the miniaturized Sentinels are inside them, eating them away.
Back on the Superdestroyer, Cyclops and Xorn are still held captive. They are held in the barrels of two cannons pointed toward the Earth. As G-Type continues the Hymn of Purification, Xorn tells Cyclops that he tires of these chains, this treatment and of restriction and death. In a moment of seeming revelation, Cyclops points out to Xorn that he possesses a star for a brain and that G-Type is composed of living solar plasma. Unaware of the information that Cyclops has given Xorn, G-Type finishes her hymn and solemnly ordains the extinction of the species Homo Superior. G-Types final statement is interrupted by her own gagging, and after a moment, she falls to the floor. The room's guards likewise find themselves on the floor unconscious, thanks to the swift action of the now freed Cyclops and Xorn. After Xorn asks Cyclops what their next move is, Cyclops simply replies that they are going to try to put things right.