Alex Summers stands with the remaining Mutant Elite Force - the Beast, the Guthries and the Bedlam Brothers - and gives the order to kill all the prisoners, like Apocalypse commanded. Beast feels it’s a waste to kill all of them as he could use the genetic stock for further experiments, however Havok tells him he is in no position to argue after letting Cyclops and Jean Grey escape. The Bedlam Brothers also voice concern and think its beneath them to kill the weak. However Sam and Elisabeth agree, after all the order came from Apocalypse himself, and if the Bedlams want to question these orders then perhaps they should be with the prisoners. Terry thinks that despite his recent promotion Cannonball is still a punk and Sam, in a rage, threatens to kill him. Havok steps in and tells them that that’s enough, there will be no dissension in his ranks.
The two pairs of siblings stop their fighting, and the Beast comments that the family feuds continue. One of the Infinites appears and reports a disturbance in sector five, caused by Cyclops, Jean Grey and an unidentified rebel. Hearing his brother’s name, Havok gets annoyed and released a plasma at the Infinite. All members of the Mutant Elite are shocked by the Infinite’s death at their leader‘ hands. Havok however asks them what they are looking at ? They have a clear order : find Cyclops and bring him his head.
In the Kennels, the hybrids and werebreeds are being moved to Beast‘s lab to be put into the gene pool. Cyclops and Jean Grey are hiding in the shadows and realize that it‘s worse than they thought, there is not much time before the killings start. They decide to take out the Brain Trust as this would eliminate the psionic broadcast that is doping the prisoners - so that they could fight back. Cyclops knows he can get them through the service tunnels to the Brain Trust but wonders whether Jean could cope with six telepathic brains against her. She tells him that after meeting Nate Grey, she feel that she is actually more powerful than she had previously thought. Jean also felt some kind of a connection between the three of them and she wonders if in another world things might have been different. Cyclops thinks that it is possible, but they can only play the game using the cards they've been dealt, and they run into the service tunnels.
However not before long they bump into the Bedlam Brothers, who figured out where they would go. The Brain Trust is the logical target and having spent so much time working with Scott, they know how he thinks. They ask Cyclops to give up as they don't want to fight. Scott replies he can't do it and he wants to fight for life not death, against Apocalypse' genocidal machinations. The Bedlams quickly discuss and decide that they'll help, especially as the amount of fun they can have has dropped recently. Cyclops is worried about them, but they feel that they can handle themselves. They tell them to go on ahead to the Brain Trust and they'll take care of the Guthries, who can be heard already down the corridor. As Scott and Jean head to their destination, Terry tells Jesse that there is no turning back now. Jesse agrees with him, there'll be no more nights uptown and after all this they're going underground, as they grab each others hand in affection.
At Heaven, Apocalypse's soldiers arrive to close down the nightclub permanently. Angel wonders whether he should actually care, as he seems to be losing staff and his many of his regular customers anyway due to Apocalypse. The soldiers tell him that he is under scrutiny and his contempt for Apocalypse verges on treason. Angel fires a flame-thrower encircling the soldiers in fire. He flies past them and heads for an elevator. After pressing the button, the doors opens to reveal an empty elevator shaft. Angel knew this day would one-day come and so created the shaft to have an easy escape route to the old subway tunnels. As he flies down, Warren realizes that he is now unable to play both sides, he is just another fallen angel who will never see heaven again.
The Guthries meet up with the Bedlam brothers, noticing that they had let Cyclops and Jean Grey go. Sam knew he was right about them and leads his sister into battle against the brothers. Terry takes on Sam and using his power, creates some telepathic static to force him into the side of the tunnel knocking him out. Elisabeth has grabbed Jesse and warns Terry to not try that trick on her or his brother gets it. However Jesse uses his power to unscrew some bolts and opens up a pipe of steam onto her face, making her drop him. The Bedlams start running and Terry says the smart move would be to get out of the city. However Jesse points out that they’d miss the fireworks, and Terry agrees, though thinks that one day they ought to give up this reckless behavior.
At the Black tower Cyclops and Jean Grey have reached the Brain trust. They decide to destroy the equipment that keeps the minds linked but the Brain Trust sense what they are up to and disable Cyclops from using his optic blasts. Jean is aware that the Trust doesn’t expect any resistance, so she directly attacks the Brain Trust telepathically. The Trust increase there telepathic attack in accordance and Jean is in agony. Remembers what Logan said about moving past the pain, Jean carries on and does not give in, too much is at stake. As the pressure increases the individual compartments that hold the brains start to fill with bubbles until eventually they explode, destroying the brain trust. Jean and Scott are covered in goop and Jean is unsure if she is alright as she has never used her powers to such a level and didn't want to kill them. Cyclops tells her that they had backed her into a corner and she had no choice. The Bedlams arrive and wonder what's next on the agenda. Jean says “A blackout“. She picked the idea from Scott’s mind, and he confirms it. Cyclops asks the Bedlams to disable the main generators.
Upstairs, Havok has Scarlett in his command post. She is held in constraints and Havok can't believe that she has betrayed him for the Human resistance. He is angry, as he actually risked his career by consorting with a human, and then she betrays him. Havok asks her why he shouldn't kill her. Unable to look him in his eyes, Scarlett replies that she is pregnant. Alex thinks its one of her tricks but Scarlett says that she wishes it was. She took the job at the club to get close to mutant officials to gather information, this was never part of the plan. Havok is really upset and tells her that this could destroy all he has gained. He starts to mention about the penalties for interbreeding when the lights go out. Alex knows that this must be Scott's doing.
Down in level 2, Cyclops confirms that the generators have gone and so have the emergency ones as well, meaning the darkness will remain their advantage. Jean tells him that the fog that the Brain Trust had put over the prisoners‘ minds is just starting to wear off, and they are beginning to realize they are free as the electronic locks have been disabled as well.
In his laboratory, the Beast is confused by the systems going offline. One of the soldiers arrives with a group of hybrids from the kennels wanting to know what to do with them. The hybrids start to get restless and turn on both the guard and the Beast. They try to kill the Beast but he claws back at them. One jumps on his back, hurting him, but he is able to knock the hybrid into the gene pool. The Beast realizes that it is time for him to get out of there and move to greener pastures.
The prisoners are running riot, without any idea of where to go. Cyclops notes that this is not what he had in mind, and when the Infinite reinforcements arrive they'll all get picked off. Jean answers that they’ll have to lead them out themselves and she telepathically links his mind to some of the stronger survivors to shown them the escape route. But before they can get far Havok blasts Cyclops in the back, telling his brother that he has pushed him to far and that he is going to die. Jean attempts to telekinetically throw a metal ladder at him but Havok catches it, reminding her that she is still weakened from the battle with the Brain Trust. Cyclops blasts at the gap between Jean and Havok so that he can't go after her. This fight has nothing to do with Jean, it’s he that Alex wants. Havok confirms, for too long has he stood in the shadow of his brother, and they start blasting at each other. They move closer together realizing that their powers neutralize each others. As they are about to be within punching distance the energies build up causing them both to be knocked back by the sheer force. Havok gets up first and walks over to Cyclops to beat him up the old fashioned way. He tells him that he wishes he hadn't been born, but Scott tells him to get over it as he two handed punches Alex knocking him out.
Jean says that Havok is only unconscious, but not dead, which could prove problematic later, but Cyclops tells her that he will not kill his own brother as his hands are stained with too much blood already. Jean says to him that the war has made everyone do things they regret, but there is a part of him that even Sinister couldn't manipulate. Jean tells him that she believes in redemption and also in him as well. Scott tries to tell her that she means a lot to him but she interrupts telling him that they can talk about it later, right know they need to get the people out of the pens. Cyclops addresses all the prisoners and tells them to follow him off the island to safety. Jean tells them that they can trust him as he stands against Apocalypse. At first the prisoners are unsure, after all Cyclops was a ranking Prelate, then again he just fought his own brother. The prisoners follow the pair to find a better world, if there is enough time to find it.
Later, the Beast‘s pet wolf wanders up to the unconscious Havok and licks his face to wake him up. As he comes around, Alex pushes the animal away and gets to his feet. He tells himself that he is going to find his brother, so that he can bury him.