In his tower base, Weapon Omega yells at Dark Beast to do the tests again but McCoy replies he has done so ten times. Jean Grey is strapped into a large piece of machinery that suspends her in the air whilst Dark Beast sits at his computers. He tells Omega that he has tries numerous different tests and they all say Jean is so human she should be put in a museum as a relic for future generations. He says he is loyal and he will run the tests as many times as he wants but they will all come out the same.
Omega tells him to stop the tests. Jean has knowledge of the human rebels, so he will need to know everything before he puts her out of her misery. With that, he orders McCoy to send for the Shadow King.
At the Shadow King’s apartment, he is stunned to see Quentin Quire stood at the door with two of Sebastian Shaw’s prostitutes. Quire tells him there is no running but the Shadow King replies that if he knew he was still alive he would have come to destroy him in person. Quire tells him that’s what everyone who is late to the party says, but this is his party and the king is dead. Quire shouts “long live the king” and promptly shoots the Shadow King’s body, causing his psychic form to leap out of it. The Shadow King jumps into one of the women who came with Quire and says that he isn’t so easy to kill. Quire then shoots the woman and the Shadow King quickly abandons her and jumps into the other woman. Quire points a gun at the woman’s head and says to face the Overmind or die a coward.
Goodnight stands in Dr. Moreau’s lab and stares at Quentin Quire’s cloned brain in a jar. He sighs and says he wishes Prophet would have warned him about it. Dr. Moreau tells him Quire’s brain is amazing and it is actualized madness; no consciousness could find its way out of that thing. Goodnight asks if that applies to the Shadow King and Dr. Moreau says it should work. Goodnight replies that for once around here he would like to hear someone say “will” as in “this will work.” With that, he takes the jar, which has belts and buckles on it, and straps it to his back like a diving air tank. He then puts a number of sensors on his head.
With the other woman dead on the floor, the Shadow King’s consciousness swirls around the room. Quire nervously asks where he is and the malevolent force taunts him by saying his arrogance is his undoing and he should have stayed hidden. He then jumps into Quire and tells him he will now feel what it’s like to have his consciousness turned out from within. Quire falls to the floor as energy bubbles around him and the cylinder with the brain in suddenly appears on his back. He stands up and sprays something on his face, revealing himself to really be Goodnight in disguise. As he surveys the bodies on the floor, he marvels that the plan worked and then radios Prophet to inform him the mission worked.
In the tunnels below New Apocalypse, Prophet says that the Shadow King has been neutralized and Jean Grey is with the Overlord. The success of her mission is humanity’s last hope. Dr. Moreau and Bolivar Trask are ready with Doom’s machine to capture the Apocalypse energy once it’s released from Omega and before it can find a new host. Horror Show asks what they should do now and Prophet replies that the Overlord has other telepaths. Jean is strong but given time they will break her down, so they have to move up the timetable. Omega doesn’t fear them but he also doesn’t have any patience. If things become inconvenient, he will try to kill Jean and that is when she will have her opportunity. Fiend says they will fight and Prophet shows the team a fleet of small, one-man flying machines. He tells them it’s no time for stealth, so he thought he would break out the big guns.
Fiend limps towards them and Prophet goes to speak to her but she quickly tells him his leg may be broken but it’s in a splint and so she’s in. As they mount the vehicles, Prophet warns them that if Jean is successful the release of the Death Seed energy will most likely level the city, if not further. Horror Show says they will kick ass until they kill them or they die. Goodnight walks in and apologizes for being late, as you can’t just stash the Shadow King in an old gym locker. He asks if it’s too late to call dibs on the reticulated battle gloves.
In Weapon Omega’s base, Jean is in another machine, but she is suddenly ejected from it and she sees Omega standing over her. She asks if he is letting her go, but he replies he is letting her out and it’s not the same thing. She realizes the time has come and he tells her he is waiting for the Shadow King as she has a lot of information he wants. She asks what will happen then and he tells her she’s human; she doesn’t even have the Phoenix Force anymore. He tells her not to worry, as she is his wife and he won’t let anyone else do it. She says it doesn’t have to be like this, the Death Seed has changed him. He tells her the Celestials enlightened him and he sees that they showed him that what she is and he was is nothing but road kill. If he doesn’t do his job, they will come back and the whole ball will go down in flames. They say mutants must evolve and it’s his job to see that it happens. Jean shouts at him and asks if he think evolution means power, because all she sees is a descent into cruelty and butchery.
Omega tells her evolution is messy but Dark Beast walks in and interrupts them. McCoy says the Shadow King is missing and when Azazel checked things out he discovered his human form had been shot. They have had no other contact from him. Suddenly, an alarm sounds and the Dark Beast informs Omega they are also under attack.
Outside, the X-Terminated are on their flying vehicles and shooting at Omega’s forces, whilst a fleet of Sentinels attack the skyscraper base. As the Sentinels slam into the walls, Prophet sets off a bomb, causing the building to explode. Unfortunately, Prophet gets the attention of Keeper Murdock and looks up to see Omega’s brutal enforcer squatting on a ledge above him. Prophet presses a button on his armor and another explosion rips out on the building Keeper Murdock was sat on. Prophet and Murdock dive out of harm’s way as the rest of Murdock’s forces are obliterated.
In Omega’s base, Jean Grey quickly puts the weaponized pill in her mouth whilst Omega is distracted by the chaos going on outside. He orders Cyclops to take down the rebels but to capture Prophet if possible, as he knows all there is to know about the remaining humans. Cyclops signs off and Omega turns from his monitor, unsheathes his claws and tells Jean it’s time. She tells him she loves him, even now, and she knows this isn’t him. She begs him to stop it all and they can be together. He tells her he was always the one who dealt with reality. He fought and, when he knew it was hopeless, he fought harder but he never fooled himself into thinking that it wasn’t to the death. He also isn’t going to fool himself into thinking she would ever want to see the end of the world.
Outside, the forces of Omega fight on the streets against the X-Terminated in a fiery battle. High above, Omega tells Jean the Celestials saw big things for this world and he doesn’t have the right to stop it. She tells him to let it be with someone else and to let go of the power and be her Logan again. He says he did what he could and he would make her a Horseman but, without her mutant gene, she is useless. This isn’t genocide; it’s survival of the fittest and he is the fittest. He says Omega Red will soon attack them from the East and asks if he should leave everything for his tender mercies. Jean starts to cry but Omega tells her to stop as she is made of sterner stuff. She replies that she isn’t crying for her, she is crying for him. He kisses her passionately and she stabs her in the gut with his claws.
As he lets her fall to the floor, Weapon Omega steps back, energy beginning to swirl around him. Bent over on the floor holding her bleeding stomach, Jean weakly tells him she gave him medicine to cure the world. He looks confused and she simply tells him she loves him as the energy around him gets brighter and brighter. Down on the streets, the X-Terminated stop fighting and stare up at Omega’s base, which is now shining like a beacon.