Smoke comes up from the main building of the Weapon X compound. In the Director’s office, someone’s voice is heard on a speaker, calling out to the Director for orders. The person describes that the attacking mutants have reached the control room and that Jackson and his agents have turned and are siding with the intruders. The soldier doesn’t get to say anything else; what follows is a load scream. The Director stands silently next to his desk, looking into a big mirror lying on it. He has listened to the report but doesn’t answer and instead he thinks about stories of Emperor Nero who is said to have fiddled while Rome burned. Still staring at his reflection, he thinks that he was never that musically inclined.
In the control room the Underground and the agents loyal to Jackson are fighting dozens of Boxbots and armed troops. One of the soldiers tries to radio for reinforcements, but he is shot in the back by Jackson. The ambitious agent tells his brothers in arms to keep it up, as once they have captured the control room, they have pretty much won. Domino however questions him, since the entire operation doesn’t go as smoothly as he made it out to be. Jackson defends himself, saying that he never told Cable it would be easy, and at the same time saves Domino from a Boxbot about to ambush her from behind. He makes a comment about the irony of the situation, as he knows that Cable told her to keep an eye on him, not vice versa. Jackson also notes that Cable is mysteriously not fighting alongside them, but Domino interrupts and says that Nate is a man who keeps his word, it’s just that he is busy with some side mission.
Meanwhile, Cable is in the hallway leading to the Director’s office and readies his weapon. He prepares to enter the room, but receives a hit in the head from behind. Turning around, Cable sees his old friend and teammate Garrison Kane, who apologizes, but announces that he can’t let Cable go in there.
In a sewer pipe beneath the compound, rogue agent Sabretooth is trying to get back into the complex and rips apart a steel net blocking his way. A number of bone needles hitting in him the back draws away his attention – Marrow, the Weapon X agent assigned to hunting down Sabretooth, has found him. She says that she used to be afraid of him, as back when she was a little girl, the surviving Morlocks told her stories about the day of the Massacre and him in particular. While these stories frightened her back then, Marrow points out that she isn’t a little girl anymore. Sabretooth couldn’t care less and unimpressed, he turns his back on Marrow, telling her that he is rather busy and has a few people to kill. As he plucks one of the bone needles, or toothpicks as he calls them out of his back, he tells her that it takes more than this to get his attention. Marrow isn’t done though, and growing claws out of her knuckles in Wolverine style, she asks if this will do. Sabretooth grins and confirms.
Still staring at his reflection, the Director thinks that everything that’s happening is his fault. He lost his edge, lost what drove him to revive the Weapon X program. His flirtation with Aurora distracted him from Jackson’s scheming within the program and from even considering the possibility of a mutant underground movement. The only thing, the Director comes to understand he was not oblivious to was his face. The Director curses and picks up the mirror, smashing it into a wall. It shatters, and Colcord look at the shards on the ground, seeing his distorted reflection in the many fragments. Almost in a trance he picks up one rather sharp shard, and looks at it, holding it up in front his face. Then he cuts himself with it; the cut is deep and draws blood. The pain gives Colcord relief, and he cuts himself again, and again, and again, and again.
In the sewage system beneath the compound, Sabretooth and Marrow are still going at each other. Creed admits that she is tougher than he thought, but leaping at him she tells him that she has no interest in his compliments. Before her claws can make contact with the man, Sabretooth grabs her by the wrists and laughs at her. He belittles her, saying that she got spirit, but that ain’t enough to... Suddenly he cries out in pain - Marrow has grown bone appendages from her wrists that bust through Sabretooth’s hands. Creed realizes that this is not the easy fight he predicted, and takes the matter more seriously. He slams his opponent into a nearby wall, shattering all her bone appendages, leaving Marrow without weapons. Shocked by the sight of her bleeding hands, Marrow is an easy prey for Sabretooth who grabs her from behind. It’s a shame, he says, that Marrow entered the Program to regain her good looks, only to lose them now. That said, he starts to scratch across her face with one of his clawed hands.
In the complex above, Kane apologizes to his old friend Cable; he didn’t want them to meet this way, and he wishes he could explain everything. Lashing out with his psionic powers, disabling Kane’s cybernetic implants, Cable asks him to explain this. He had known about Kane’s inferiority issues, but never would have thought that they’d drive him to become part of the twisted Weapon X program. Standing over the collapsed form of his former comrade, Cable recites how he was like a brother to him, taught him everything he knew, fought besides him and saved his life only to see him turn “stormtrooper for these nazis”. Turning his back on him, Cable says he’d rather see him dead. He fails to notice the glow in Kane’s cybernetic eye, indicating his systems rebooting.
Cable kicks in the door of Colcord’s office, shouting it’s over, when he becomes aware of the Director’s unconscious form lying in a pool of his own blood. He kneels down and tells him that he won't let him get off that easy, not with all the secrets still in his head. Despite having trouble keeping his telepathy under control, Cable enters the Director’s mind to learn what Neverland is. The images he finds are of tortured and killed mutants held in a concentration camp and they sicken him to no degree. Calling the Director a bastard, Cable asks how he could do it. In the name of mutantkind and all his victims, Cable condemns his actions as crimes against humanity and points his gun at him, ready to shoot. Suddenly a tendril wraps around the gun, and wrests it from Cable’s hand. Cable turns to see who intervened in his actions, and is surprised.
By now, the other Underground members and Jackson’s little group have secured the control room and effectively dealt with all Boxbots. Jackson however reminds everyone not to get overconfident, and he finds his suspicions confirmed when Blaquesmith, operating one of the computer consoles, shows him that Room X has been breached. Jackson tells the others that a very dangerous wildcard is loose, and right on cue, the unconscious Cable is dumped in front of them by Madison Jeffries. Wearing an exo-skeleton of his own design, the former Alpha Flight member called Box carries the Director with one set of arms, while with the other he points to the huge army of Boxbots behind him, saying that Jackson is not the only one who has friends.
In the sewage system, Sabretooth still has Marrow in his grip, and once more getting careless, he gloats on how it’s not often to get the chance to get one of the ones that got away. Marrow struggles in his arms, and forms a bone stick in her left hand. All of a sudden, she breaks free and rams her creation into a valve on the wall, using it as leverage to open it. As she does so, she tells Sabretooth to say goodbye. Creed is too late to react, and finds himself face to face with a floodwave of incoming water. It washes him out of the sewers, while Marrow clings to the valve, not letting go of her bone. Once the water has passed, she walks to the end of the pipe, and looks down the mountain wall – no sight of her opponent. “That was for the Morlocks, you bastard!” she says.
Alerted by Domino, Cable comes around and finds himself surrounded by the battle. The Underground members and Jackson’s group are busy fighting Boxbots as well as they can, but Jeffries is capable of replicating them faster than they can keep up. Even worse, Cable finds that he is immune to a telepathic attack. Unexpected help arrives in the form of Garrison Kane. Entering the room through a hole in the ceiling, Kane says that Cable was right about him, he did let his insecurities overwhelm himself, maybe even so much that it is too late for him to do the right thing. However, Kane says, it’s not too late for him to end all this, by downloading the one power that will kill him. Right as he joins the heroes in their attack against the robots, he activates his systems to download the technomorphic abilities of Madison Jeffries. Kane smiles at his old friend a last time and says goodbye.
What happens next is a sight for itself, as Kane takes mental control of nearly all the technological equipment in the room, absorbing it into himself. Jeffries knows that he is fighting a lost cause, and calling up a metallic wall to cover their escape, he leads the still weakened Director out of the room. Despite the imminent danger to both of them, the Director tells Jeffries to hurry, as they have one more stop to make.
Having absorbed all that equipment, Garrison Kane is no more. What’s left in his place is a deactivated, metallic being, the expression on it’s stiff face that of pain. Cable touches it and tells his friend goodbye, while his teammates silently watch. Jeffries interrupts the touching scene, saying that Kane’s sacrifice sure came unexpectedly, but they are all full of surprises. “Vive le resistance”, he says, and with his words he triggers the compound's main computer, which he previously rigged to affect the brain area that control telepathy. All present collapse to the ground, Cable putting up little more resistance than the others, but it’s no use and he too goes down. Now talking to himself, Brent Jackson thanks his special ear plugs to shield him from the computer’s dampening effect, and comments on Cable’s suspicions not to fully trust him having been the right notion. However, whatever suspicions Cable had about him, they won’t do him any good now.