Sam is carrying Storm and Lady Deathstrike to the center of Mt. Haven when an unknown force attacks the three of them. Sam thinks to himself of how he knows what lightning feels like and this is far worse. They are not the only ones that have been attacked by this electricity to their neural net, so has nearly every mutant in Mt. Haven, including Sage. Bishop lays her body on the ground as it convulses and he looks up to see the other mutants of Mt. Haven writhing in pain too.
Suddenly, Bubbles falls nearby and Bishop asks her what is happening. He does not get an answer, as Bubbles explodes only a foot away. Bishop surmises that his theory was correct and the entire town’s neural net has been replaced by nannites. Luckily, he thinks, Sage has not been there long enough for her entire neural network to replaced. Bishop checks for a pulse and realizes that Sage is still alive. Just then, the door to the nearby inn opens up and the Garza family steps forward. They tell Bishop that their son and daughter are feeling strange and Bishop tells them that the two of them should be fine after a little rest. The Garza daughter looks up to see Sam swaying in the air by the pain of his recent events and she warns Bishop of his approach. Sam loses grip of Deathstrike and she falls through a nearby mansion’s ceiling. Sam does not make it much farther as he and Storm collapse to the ground in front of the very same mansion.
Meanwhile, in the catacombs of Mt. Haven’s lower complex, Stryker talks to the apparently dead Kitty about how he must sacrifice some good to prevent the bad. He tells Kitty that he believes she is good and he hopes that her sacrifice will help them win the war. Leaving the room, he touches a button on his neck collar, which causes Kitty’s Mandroid armor to engulf her face.
Meanwhile, above Stryker, Bishop explains to Sam about how they all survived, thanks to the process of neural pirating had not been complete. He explains that the reason he was not affected was because he was inoculated against the nannites in boot camp where he was from.
Back in the catacombs Stryker is startled by a noise as he walks up the stairs away from Kitty’s body. He tells himself that he is nervous and that maybe a Psalm might help him. He begins to quote Psalm 23 as he walks and Kitty surprisingly floats through the floor knocking Stryker to the ground.
Sam has decided to go after Wolverine’s body and, upon his arrival, Sam finds Logan awake. Shocked but glad, Sam helps Wolverine to his feet. Logan explains that he smelled something in the air when he battled Lady Deathstrike and he knew he couldn’t fight both the virus and her at the same time. He decided to take the fatal blow and hope his healing factor could bring him back and set his body right at the same time. Sam grasps hold of Logan and the two of them fly off, with Wolverine explaining that they must find Kitty.
In the catacombs, Kitty pulls out the gun she had obtained earlier and, holding it to Stryker’s head, she quotes Revelations about the fourth seal, death and the pale rider. Stryker tells her that he cannot kill her, because she is an X-Man and they do not kill. She tells Stryker that she is a Chicago girl and she plays by hometown rules!
Outside the mansion Deathstrike has fallen in, a bomb is thrown from the inside. Sam and Logan notice the projectile and Sam acts fast to stop it. He drops Logan into the awaiting arms of Bishop and grasps the bomb in his hand. He flies off into the sky, thinking that, if he keeps blasting, the bomb should not be able to hurt him. Sam is right, though the bomb does throw him quite far back into Logan’s arms. Bishop uses his powers like a machine gun to blast away at the building in hope to distract Deathstrike. Logan tells Bishop to handle Deathstrike by himself, while he deals with Stryker and Kitty.
Inside the entrance to the catacombs in the church, Logan talks to himself and says that Kitty always said he was the conscious of the X-Men. He just hopes he doesn’t have to be hers. At the same time, at the bottom of the catacombs, Reverend Paul resurfaces as the lights come back on. Paul walks down the stairs, seeming to fade in and out like a television out of tracking. Kitty tells Paul that they are all children of God and, just because his gifts won’t allow him to see the light in humans, it doesn’t mean they are bad or deserve to die. Paul tells Kitty that humans act like enemies and come to kill mutants.
Wires burst into lines of electricity all around them and Stryker tells Kitty that Paul will be nothing but a ghost in mere seconds, because the systems are crashing. Kitty runs after Stryker and tells him that Paul isn’t crashing he is trying to send his conscious out into the world’s computer network. She explains that Paul is now as human as they all are, because he has become a Cybernetic sentient; a true artificial intelligence. Stryker exclaims that there are no lines out, but Kitty reminds Stryker that Deathstrike is a walking computer that Paul can use.
Inside the mansion, Bishop searches for Deathstrike, realizing the truth about Paul and how he can use Deathstrike to cause global turmoil. He wonders, as he sees Deathstrike’s hand lying from under a rock, how he will be able to stop her, since he will have to destroy every piece of her to stop Paul. Bishop leans down and picks up the arm wondering if he is to late.
Paul’s computer-like flashback
Back in the catacombs, Paul talks to Kitty about the times when Paul was a prisoner at Mt. Haven and he (being the artificial intelligence) would talk to Paul. He learned the light from Paul and how only Paul had it and the others around him did not. The computer talks about how Paul was examined by the humans and experimented on. It tells Kitty that Paul knew it was the reason for Paul’s pain, but Paul did not care. It tells Kitty about Aaron Pankow and how it pleaded with Aaron to allow it to help Paul, but he wouldn’t let it. So it decided to take control, but Aaron hurt it and suddenly there was a great light and it found itself joined with Paul. With the computer now in control of a body, he decided to atone for all his sins and help others like him now peace.
Almost in tears, Paul cries out in wonder about what he has done. Muttering to himself, Stryker states a verse from the Bible that talks about that which is born of spirit is spirit and, except a man be born, again he cannot inherit the kingdom of God. Above them, Wolverine runs out of the church as hundreds of pounds of wood and metal come crashing down.
Kitty commands Stryker to leave the catacombs and to tell the others to evacuate the valley, because she is going to use her powers to collapse the thermal batteries and destroy the town. Stryker tells Kitty that he is willing to sacrifice himself, to let Paul absorb into him so the both of them can be trapped under the town. He explains that if Paul was to get a hold of her powers, he could wreck havoc across the globe. He tells her that Paul seems to need a teacher and so does he maybe by joining together the two of them might teach one another. Kitty agrees and Paul fuses into Stryker. Stryker lays back into a holding cell and tells Kitty to lock him and throw away the key. As the latches close, Stryker asks Kitty why she is smiling. Kitty tells Stryker that, for the first time in Stryker’s life, he is calling a mutant a “him” not an “it.”
Above the ground, Wolverine watches as the church sinks into the ground. He is saddened to know that one of his best friends was below all the rubble. Shockingly, Kitty phases through the ground and tells Wolverine that everything is going to be okay.
In the Chicago club called Belles of Hell, the X-Treme team listen as a report comes in on the television about Stryker’s disappearance and the volcanic slide in northern Washington. Logan toasts Bishop for blowing the thermal reactors and they talk about Stryker and how he wasn’t evil after all, just misguided.
Storm and Kitty are on top of the bar’s roof and Kitty tells Storm that she is tired of hiding behind costumes and Xavier. She tells Storm that there is an election at her school coming up and she plans on running for Alderman. Just then, Logan walks out onto the rooftop and he teases Kitty about her running for politics. The three of them sit on a ledge of the roof and Kitty tells them that all three of them have ridden the pale horse and survived. Logan puts his arm around Kitty and tells her that he doesn’t want that to be his epitaph. Storm puts her arm around Kitty as well and she tells her that she wants Stryker and Paul to wake up to a world that was worth their sacrifice. Holding their beer bottles high in the air, the three friends toast an “AMEN” to that.