In the desolate center of the Nevada Desert, alarm bells are ringing in Dr. Moreau’s hidden lab. The apparatus that he and Bolivar Trask built to capture the Apocalypse energy has suddenly leapt into action. As the men rush around the various consoles and instruments surrounding the machine, Bolivar wonders if Weapon Omega is dead. Dr. Moreau says he has no idea, as people keep him in the dark about so much, but the readings they are getting are massive. He would be shocked if New Apocalypse wasn’t about to be wiped off the map.
In New Apocalypse, Jean Grey had gotten close enough to Omega to use the pill that caused the breakdown between his cells and the Apocalypse energy. Omega was dying but the energy escaping from him was enough to level the city itself. On the streets below Omega’s base, the various citizens were now running for their lives, as the energy being released was lighting up the whole sky. Everyone expected to die but it was the price they would pay to free the world from the tyrant. In the Nevada Desert, the two scientists constantly checked the apparatus to see if the energy had been captured before it could find a new host.
The Apocalypse energy had other plans, though, as Jean Grey herself was now radiating energy, despite the mortal would Omega had inflicted on her. As Omega kneels on the floor, he tells Jean that the energy sees that she used to house the Phoenix Force and she would be perfect for it. As he bleeds from numerous wounds, he tells her he is sorry, as he didn’t want this for her. She looks at him, gets angry and screams “no” as the energy pulses around her. Omega’s base explodes in a huge fireball that levels the building and some of the blocks around it. When the dust cleared, though, the city still stood and the real disaster had been averted. No one knew why, and many didn’t even know what really happened anyway. Everyone could sense things would be different now and forever more.
Soon after, Penance addresses a large crowd of people who had gathered on the streets. She tells them tragedy has been averted and tens of thousands of mutant lives were saved. She calls them all to rally to her, as the old dictator has fallen and they are now in a brave new world. It’s time to reshape the world not in the image of the Overlord, a savage butcher who lived to be cruel, but in her image of beauty, kindness and penance. As she floats high above them, she tells them she will be their salvation.
In the tunnels beneath the city, some of the X-Terminated gather to take stock of recent events. As Prophet tends to Deadeye’s cuts and bruises, Goodnight says that Penance has rallied everyone around her. Deadeye asks if they should find Fiend and Horror Show but Prophet tells her no, as things are happening too fast. The energy has left a strange ionic interference and all the communication lines are down. He can’t contact Bolivar to check if the energy is contained and he doesn’t even know if Weapon Omega is dead. Since they are still alive, then it is possible he isn’t and Deadeye suggests there might even be a new Overlord. Prophet says that’s what he needs to determine and then tells her to stay and watch Penance’s rally. He tells Goodnight he needs to go back to the Hellfire Club again, because if there’s anyone who would know if the Overlord’s alive then it’s Sebastian Shaw. Deadeye asks Prophet what he will do and he simply replies what he has to.
On the streets, Penance and Colossus hand out food and clothing to the crowd as Deadeye scales a wall nearby. Penance tells Colossus it will be dark soon and she doesn’t want her people to go cold and hungry. As she picks up a small mutant baby, she says there will be no more war dogs, gene pools, secret police and hounds. Under her rule, they will all live free from the highest alpha to the lowest dreg or human being. The crowd seems shocked to hear her say she will help humans and she replies that they owe a lot to the lowly Homo sapiens. They must all pity their plight as the time for hate and fear is in the past.
Penance is suddenly hit by a beam of red energy and she is catapulted to the ground. On a nearby tank, Cyclops and a bunch of soldiers stand over the crowd. He yells for them all to get back to their homes and anyone on the street in five minutes will be an open target. He asks Penance if she thinks she can just move in and take charge. The government is still in charge and order will be restored. If their Overlord cannot be found, then a new one will emerge. From the floor, Penance looks up at Cyclops and tells him that he had better hope Omega shows up soon or else it will be too late to save himself.
Prophet runs through the tunnels when he runs into Fiend, who tells him that Horror Show got her down there during the big light show. As she limps towards him, he helps her walk and he says that he knows something has happened but he doesn’t know what. He asks where Horror Show is and Fiend replies that, after he dragged her into the tunnels, he gave her a gun, kissed her on the head and then left. He was bleeding pretty bad but trying hard not to show it.
Horror Show staggers back through the tunnels and comes to the beaten and bloodied body of his father, Sabretooth. As he crouches down, he says he thought he would be the one to do this to him but it turns out he did it to himself. He sarcastically thanks his father and then takes his gun out of his holder and puts it to his head. As he is about to shoot himself, though, he hears a small whisper coming from Sabretooth and so he leans down close to listen. Sabretooth whispers again and Horror Show puts the gun back and calls his dad a bastard.
(the Hellfire Club)
Goodnight, dressed in his Hellfire Club clothes, walks into Sebastian Shaw’s office and takes a seat across the desk from him. He cuts straight to the point and asks if he has heard any rumors of the Overlord’s survival. Shaw says he has no news but he does have information pertaining to him. Goodnight smiles and says he never laid a hand on her, whoever she is. Azazel teleports in and Shaw says that the minister has told him something about him he hopes isn’t true. Azazel looks to Goodnight and tells Shaw he is the one of the human rebels he saw in Latveria.
Back on the streets, Penance tells Cyclops that they will not go back to their homes and she gives them all one chance to lay down their weapons. Havok laughs at her and asks if he should release his dogs to give the dregs a lasting lesson. Cyclops tells Penance she has one minute to clear the streets.
On a building above, Deadeye watches the scene through the lens of her sniper rifle and she radios to Prophet that things are about to get ugly. He tells her to make sure it does and so she fires a shot, clipping Cyclops around the head. Havok sees his brother go down and he yells to the soldiers to teach them all a lesson they won’t forget. The two sides both charge at each other, with Colossus calling for the death of Omega’s gang.
Down below, Fiend tells Prophet that people are dying because of him now but he replies a civil war was inevitable. She tells him that’s just an excuse and he admits it is, as he needed everyone away from the site. As they climb up through the sewers, Fiend asks if he thinks Jean or Omega might be alive and he says he hopes not. It would mean Jean has failed or worse, the Death Seed has taken her over and she is the new Overlord. As they reach the surface, they see the devastation from the explosion as a number of samurai sentinels watch over the area.
Colossus and Penance continue fighting Omega’s forces and he tells her that they will prevail, despite how many they have to take out. Penance says that she is sick of blood and her reign shouldn’t begin like this. Havok goes to his bleeding brother and tells him not to worry, as he will handle this his way. One of the soldiers gets Havok’s attention and tells him there are too many dregs and he has called for reinforcements. As he says it, Deadeye lines a shot up on Havok’s forehead but she misses and shoots the soldier clean through the skull instead. Havok spots her and hits the building she is on with a plasma beam.
At ground zero, Prophet finds the bodies of Jean and Weapon Omega lying next to each other amongst the debris. He goes over to Jean and a small blade flicks out from above his wrist. He is about to kill her but Omega stops him and says that she funneled the power through her and away from the city and then rejected it. Prophet asks where he stands and Omega replies “on two legs,” as he gets up and walks away.
The apparatus suddenly springs into life as Dr. Moreau declares they have harnessed the Apocalypse power.