At the New Mutant Leadership Institute, Dr. Garrison has cornered Shan and Doug Ramsey and turned his pheromones powers against them. Rather than finish them off, he toys with them a bit by making them intensely in love with each other and then consume them in a jealous rage. As he schemes up the most evil way to kill them and destroy any evidence of his connections to Project: Genesis, Tag arrives and tags Dr. Garrison, causing him to be compelled to run from himself.
When Garrison sees himself in the reflection of the window, he throws a chair through it and turns to run. When he then sees himself in the computer screen he launches himself through the window and plummets to his death. This shocks Brian, as it was not his intention to kill Garrison. Karma thanks Tag for saving their lives and expresses her regret that Garrison killed himself. Tag feels guilty but wonders if Garrison was such a threat, should they be worried about Laurie, too given how close she and her father were.
At Project: Genesis, Laurie has used her pheromones to induce a killing rage in all those present. The Hellions and New Mutants rivalry has been heightened to the point of murderous intent and the terrorists are also coerced into attacking their would-be mutant accomplices. As the battle rages, two humans kill each other and another throws a grenade at Quill. Synch sees this and dives on it to save his teammate.
Mercury is unaffected by Laurie’s pheromones and confronts her about why she is doing this. Laurie considers turning someone specifically against Cessily but doesn’t since they were roommates and best friends. Laurie admits that even SHIELD is oblivious to her father’s true efforts and decides that since she can’t kill Cessily herself, she’ll coerce the terrorists into doing it for her.
Elsewhere, Nori confronts her father and Prodigy squares off against Scion. Nori evades her father’s attack and goes after Scion. Seeing that Julian needs more room to effectively deal with his attackers, Illyana teleports them all away. Laurie continues to toy with her victims, this time turning Sooraya against Jubilee and allowing Jubilee enough free will to realize that she’d being attacked by her best friend. Sooraya claims that it was Jubilee’s influence that made her abandon her values and faith. Jubilee resists defending herself against Sooraya’s sandstorm. She refuses to kill her friend. Just as Jubilee voices this sentiment, Mercury forms a blade and kills Laurie. As she runs Laurie through she tells her friend that she didn’t give her any choice.
Illyana transports Prodigy, Surge, Scion and herself to the heart of the volcano where they continue their struggle. David comments on her sword which she claims SHIELD located in the mystical realm that is tied to her powers. She attacks David with it but Nori blocks the swing and sends an electrical charge through it that subdues Magik. This distracts David long enough for Scion to get in a telekinetic shot at Prodigy.
David falls towards the lava and certain doom but is caught at the last moment by Julian. Julian tells David that he never liked him much but he didn’t want him dead. Now that they are out of range of Laurie’s pheromones, they are all back to their normal selves. Nori, however, is still ailing form the damage inflicted by the SHIELD agents who were torturing Cameron Hodge. Both Magik and Scion are surprised to here that SHIELD has torturers on their payroll. Despite their concerns about SHIELD, the group turns their attention to stopping Laurie.
As Mercury cradles Laurie’s body, Wind Dancer clears the air of her pheromones. Sooraya apologizes to Jubilee as Sophie uses her powers to telepathically calm the human terrorists. Magik arrives and Scion reminds everyone that they are all on the same side now. As he speaks, Sophie is shot in the back by Donald Pierce who sees the mutants as expendable now that they’re inside Genesis. Seiji disagrees with Pierce and insists that they all work together. Pierce threatens to kill Seiji himself before allying with the mutants. Moonstar steps in and engages Pierce in single combat. The other mutants use this opportunity to shut down Genesis. Looking about, David and Julian realize that they’ve led their friends Sophie and Synch to their deaths.
With Sophie’s death, Project: Genesis’ mutant guards are free to act once more. They attack and kill Quill. This drives Scion into a murderous rage and he snaps one of the guards neck. Moonstar continues her fight with Pierce who taunts her by asking how she lost her eye. She responds that a sapien took it and paid a high price as a result. Pierce claims he won’t be such easy prey as he slices open Dani’s abdomen with his blade. She grabs his arm and drives the knife through his neck, killing him in one move. Julian sees the death around him and realizes he is a failure as a leader. He worries that Sofia will be the next team member he gets killed. She assures him that he’s a good leader and these deaths were not his fault. David reminds him of why they are there and the remaining mutants begin to take Genesis apart.
Together, they dismantle the equipment and free Genesis’ victims. As they are doing so, a noise can be heard overhead. Above the labs, Emperor Sunfire has arrived with a group of SHIELD agents and a small contingent of Sentinels. Sunfire offers them a chance to surrender. Realizing that if they do that the truth about Project Genesis will never be revealed, the group decides on their course of action. Magik will teleport the surviving test subjects out of there and will blow the whistle on the project publicly. The rest of the team will buy her enough time to get away by taking on Sunfire and his forces.
Surge provides a distraction and makes it clear to Emperor Sunfire that she is not his child, but a rebel like her father. Together Scion, Prodigy, Jubilee, Wind Dancer, Surge, Mercury, Dust, Moonstar and Seiji Ashida topple the statues of Emperor Sunfire and Lord Magneto and lead a direct assault on Sunfire. As they charge, Sunfire orders their deaths. At that precise moment, the reality-bending wave of energy manifests and things revert to the way they once were. Or do they?