Most of the mutant population has been decimated due to the Scarlet Witch's powers. Once 182 students are now only 27 including X-23 who Wolverine urges to come due to the fact that the world has gotten a whole lot scarier for mutants. Wind Dancer, Prodigy, and Tag are only 3 of the students depowered. Prodigy shows the remaining members of the Hellions and New Mutants squads followed by X-23 the danger cave, and Wither hasn't been seen since he touched Wallflower's hand (thinking he was depowered) leaving her in the infirmary. A depowered Wind Dancer is shown packing. Throughout the story arc, Reverend William Stryker is seen recruiting specific people to join his purifiers.
In the middle of an argument between Scott and Emma, Icarus shows up at the door with his wings amputated revealed to be by Stryker. Elixir attempts to heal him but is needed in the danger room for something important. Emma responds to the decimation by disbanding all the training squads which most of the members of the squads already depowered, and has a battle royal between the remaining students in the danger room with Wallflower, Gentle, Blindfold, and Ernst being excluded and Stepford Cuckoos excluding themselves. The students chosen to be X-Men trainees were Surge, Hellion, Elixir, Rockslide, Dust, Mercury, and X-23 added by Cyclops. Emma makes another announcement that all depowered student will be leaving the institute, but after they board the bus a missile explodes it.
Forty-two former students died on the bus explosion. The remaining students mourn those that died at the funeral of Brian Cruz (Tag). At the end of the funeral, Hellion is disappointed to hear Wind Dancer left and Elixir is disappointed in himself for not being able to help the depowered students. Emma tells the New X-Men to move on and meet her in the danger room. A couple of the younger students watch as the New X-Men face off against Colossus in the danger room. In the infirmary, Wallflower explains her concerns for Elixir to Cannonball. He replies by telling her to talk to him. While they are talking Icarus(still refusing treatment for his wounds) sneaks out of his room. Back in the Danger Room, Colossus easily defeated the New X-Men which angers Elixir in which he attacks Colossus asking him why he couldn't have saved them. Emma immediately throws him off the team for his actions. Reverend William Stryker is shown identifying two threats that need to be taken out: Wallflower and Elixir.
Inside the institute, Icarus Is shown confiding in Dust telling her he is going to fix what went wrong and gives her an address. This confuses Dust and X-23 tells her not to trust Icarus because he smells of death. Outside the Institute, Wallflower attempts to comfort Elixir by telling him the deaths of their classmates were not his fault. This only angers Elixir and the two get into an argument. As they argue a sniper (Matthew Risman of the Purifiers) shoots Wallflower in the back of the head. It is revealed by Stryker, that Dust is the next target. Icarus shows up at Stryker's church. While he is questioning Stryker's promise to save his friends, Stryker walks him into a room with an online Nimrod Sentinel.
Stryker reveals his plans to Icarus who in response yells at Stryker. Back at the institute, X-23 offers her help to Dust before she leaves. Dust denies her request because she trusts Icarus. In the headmaster's office, Cyclops reveals to Prodigy that he will be staying at the institute even with the loss of his powers. As he tells him this, Beast charges in telling Cyclops that there's been another attack. Outside, the rest of the school is shocked to see Wallflower dead as Elixir cries and Surge cradles Wallflower's lifeless body in her arms.
Back at Stryker's church, Stryker reveals his visions of Wallflower and Dust to Icarus and his reasons for having to take them out. During their conversation Dust arrives and Stryker gives his Purifiers the go to take her out. They rifle Dust to the ground as Icarus begs for the life of his friend. Then, Stryker pulls out a gun and points it at Icarus. He tells Icarus that he is about to reunite with his girlfriend, Julia Cabot, who is surely waiting for him in hell for loving a mutant. Icarus calls him a monster and Stryker shoots him.
Back at the institute, the X-Men leave in teams each taking a sentinel; Emma Frost, Beast, Cannonball, and Bishop remain at the Institute with three O*N*E* sentinels. In the infirmary, the rest of the students tell Elixir that Wallflower's death wasn't his fault as they too are saddened over the death of their friend. An explosion occurs and alarms the remaining X-Men and students. It is Stryker and his Purifiers who arrive at the mansion and take out the remaining sentinels using the gauntlet from the Nimrod sentinel that is now on Stryker's right hand. With the sentinels down Stryker declares that tonight they will win the war between heaven and hell.
Back at the Stryker's church, two Purifiers dispose of Dust's body which at that moment wakes up and attacks them. It is revealed to be X-23 under the burqa. Inside the church, the remaining Purifiers realize it is taking them too long to dispose the body and are also worried about the current power level of the Nimrod sentinel. Just then, the Nimrod sentinel comes online and terminates a few of the purifiers as Icarus bleeds to death on the floor of the church.
Back at the institute, Pixie and Anole run down the hallway to find out what's going on and ask Quill to join them but he refuses. At that moment, a Purifier shoots Quill leaving him dead. In the infirmary, Prodigy tells Elixir to stay with the deceased Wallflower as he finds out what's going on. He meets up with the Stepford Cuckoos who are having trouble finding out what's going on. With their telepathy they manage to identify Stryker as the source of the attack and that Stryker himself is in the mansion. At that time, Hellion and Surge rescue Emma from one of the Purifiers and Dust wakes up in just her undergarments and helps Mercury and Rockslide (who is supervised to see her without her burqa and niqab on). The Purifiers see her and are shocked that she is still alive. Dust then assumes her sand form and kills them.
Outside the institute, a Purifier points their gun at Surge and X-23 arrives with the New X-Men and saves her taking out the rest of the Purifiers. Dust asks X-23 why she took her place and X-23 replies Allah did not want Dust to die. X-23 then takes a psionic baffler device off of a Purifier so that Emma can read his thoughts. Emma finds out that Stryker was behind all the casualties: Icarus's wings, the bus explosion, and Wallflower's murder. Elixir becomes enraged after hearing that Stryker was responsible for Wallflower's death.
Inside the institute, Prodigy sends a message to Emma via the Cuckoos that they need help and are engaged by Stryker and Dr. Abrams. Stryker orders Abrams to kill Prodigy and the Stepford Cuckoos, but Emma Frost and the New X-Men arrive and Stryker is shocked to see Dust still alive. Dust calls Stryker an abomination and he replies back that he will not fail the lord. As he prepares to strike them with the nimrod gauntlet on his hand, Elixir shows up. He touches Stryker immediately killing him as his skin turns from gold to black.
In the aftermath, the O*N*E* soldiers and med teams assess the situation and Cyclops checks up on Emma who is depressed over the deaths of her students. The students are in shock of Elixir's new found power as Prodigy wonders if Elixir's powers were ever supposed to kill.