On the outskirts of Manhattan Island, five prisoners are trying to escape the pens when Sinister's Elite; Cyclops, Havok, Aurora and Northstar stop them. Cyclops, Leader of the Elite, tells them to surrender, but one of the prisoners fires a seismic shock and the prisoners try to outrun the elite. Cyclops takes down Dominic with an optic blast. Although he burns himself every time he uses his power, Pyro attempts to take out Havok by smashing his bike, but Havok retaliates and kills him for the damage he did to his bike. Northstar catches up with Newt and rather than waste his energy powers, beats him up severely with his fists. Aurora catches Phantazia who begs to be killed rather than go back to the pens. That leaves only one prisoner – Artemis, and Cyclops is already searching for her, but her mutant power to camouflage herself make the search rather difficult. Suddenly Artemis reveals herself and kicks him to the floor. After a brief struggle Cyclops pins her to the wall. He tells her that he doesn't want to hurt her and she shouldn't have refused Sinister's invitation to join them, however she disagrees and pulls out a knife from her sleeve. Just as she is about to slash Cyclops, she is killed by a blast from Havok. Cyclops tells him that he didn't have to kill her, but Havok disagrees, its survival of the fittest.
Where once stood the statue of Lady Liberty, now stands a statue of Apocalypse. From the base inside the statue, Sinister looks out from the 'eye of Apocalypse' contemplating his betrayal. Sinister has spent several years engineering his plans for mutant evolution in his image only to see it be threatened by Apocalypse's plans for world war. He plans to leave his Elite force to their own devices. Sinister hopes that Magneto’s X-Men will distract Apocalypse and the other Horsemen long enough for him to carry out his plans. He knows Cyclops will hate him for deserting him, but if it wasn't for him the plans he has made wouldn't be possible.
Apocalypse had entrusted Sinister with the creation of the next generation of mutants, not by accident but by design. He built the pens to store humans and mutants for his genetic stockpile. Sinister thinks that although the inmates of the pens have been spared from certain death among the cullings, they still continue to rebel, though it’s nothing his troops can’t handle. Sinister thinks back to a Kentucky culling where he found the Guthrie siblings, three of them mutants. Although their sister Paige refused to join, Sam and Elizabeth became part of his Mutant Elite Force as Cannonball and Amazon. As they put back some of the rebels back into their cells, Alex and Havok return from their successful mission. Seeing Sam about to beat up some of the prisoners, Cyclops stops him and blames him for the escapees from earlier, as it happened during Cannonball’s watch. He tells Alex to keep him in check as he walks off to talk to Sinister. After Scott has left, Alex tells Sam that unfortunately Cyclops is head of the Elite and he has to put up with him - for now.
In a lab deep within the complex, the Beast is huddled over one of his consoles when his pet wolf alerts him to someone entering. It‘s Havok, who Beast welcomes warmly in and asks if Havok is experiencing any after-effects from having some Sentinel parts been removed from his body after they got fused to him during a transporter mishap. Havok says he is fine, he just wants to check if the mutants they stopped earlier have been sent to the Beast, which they have. Beast tells him how grateful he is, since the Kelly pact restricted genetic experimentation he has had problems finding source material. The bodies of the five escapees are tied to a long chain, which he lowers the bodies into a gene pool, where they are broken down into basic protoplasmic soup. From this supply, the Beast can take nucleotid sequences as he pleases and designs the many Infinite soldiers, though they only have limited lifespan. Havok changes the topic and tells the Beast that he thinks his brother's judgement is impaired, and that he wonders that if change occurred what his opinion is. Beast retorts that as long as he can continue to work in his labs, he has no problem with change, however he warns him that Cyclops is held in high regard by Sinister.
At the same time, Cyclops is walking down a corridor when suddenly the Bedlam brothers crash through a door whilst fighting each other. They see Scott and stop fighting, as they have been just fooling around. They ask him if he wants to go to Heaven with them later that evening, but he declines explaining that he wants to see Sinister. They leave and Cyclops actually envies the bond the two brothers share, as he and Alex have never been that close. Scott carries on to the door of Sinister's sanctum, which is guarded by a so-called gatekeeper, a disembodied telepath mind floating in a sphere filled with a liquid substance. The gatekeeper informs Cyclops that Sinister is currently unavailable, leaving Scott puzzled about his mentor’s whereabouts. Sinister overlooks from inside his office. Talking to himself he says that Scott failed to realize that their last meeting was an good.-bye and that he has set him free.
That evening, Havok arrives at the nightclub Heaven, which is a neutral ground for both humans and mutants. Alex is greeted by the Bedlam brothers, who offer him a drink, but he declines as he has other plans. He bumps into Angel, the club’s owner, and he questions him about a certain cajun traitor being there recently and how he would hate to shut him down. However Angel is having none of it and tells him that he thinks something else than the drinks and the music keeps Alex coming back as he looks at the singer on the stage, Scarlett McKenzie. Suddenly her show is interrupted by Henry Gyrich who shoots several times to get everyone’s attention and then announces that he will as a suicide bomber to make a stand against mutant rule. However before he can do anything, the Bedlam brothers confuse him and destroy his weapons, as one’s powers allow him to control machinery and the other can effect minds. Scarlett asks the crowd for a round of applause for the bedlam brothers before finishing her act. She leaves to her backstage room, where Havok is waiting and they embrace.
Later that night, the three Elite return to there base and are met by Cyclops who expected them back over an hour ago. Jesse makes a joke about Havok getting lost backstage with the attractive human and Havok tells him to watch his mouth. Terrence calms Alex down as they know the penalties for miscegenation. Cyclops takes them to the door of Sinister's sanctum and tells them that something is wrong as his comline has been down for days. Terry scrambles the brain of the gatekeeper so they can get in, only to find the place has been virtually destroyed. Alex wonders if the X-Men did it but Cyclops tells them Sinister must have done it himself and abandoned them, betraying Apocalypse. Jesse wonders who should run the show now that he has gone and Terry thinks it should be Scott, who reluctantly agrees. Havok thinks to himself that it will change very soon. Sometime after they leave an auto destruct sequence is engaged and the head of Apocalypse's statue explodes.