After the attack by the Underground on the Weapon X facility, Aurora has flown herself, Malcolm Colcord - the former director of the Weapon X project - and Madison Jeffries to safety. She flies at full-speed, and his freshly disfigured and bleeding face covered by a towel, Malcolm thinks to himself what a ridiculous situation he's in: he's being rescued by the people he hates most - mutants. Aurora smiles and stops flying, suddenly dropping Malcolm and Jeffries harshly onto the ground. Malcolm demands to know what she's doing, because this isn’t anywhere close to the destination he told her to fly to. Aurora gets angry stating she knows that. Suddenly using her super-speed she punches Malcolm’s face several times.
Jeffries tries to stop her, but Aurora knocks him back and he loses consciousness. Aurora rushes back to Malcolm and uses her super-speed again to run circles around him, and creates a tornado to lift him up. Actually all Weapon X agents are equipped with mental chips that inhibit them from attacking a superior, but as in Aurora’s case it no longer works, Colcord realizes that she must have developed a third persona, different from the introverted “Jeanne-Marie” and the extroverted “Aurora”. Colcord knows that this persona is extremely dangerous, but also that he is responsible for it, for it must have emerged to cope with the recent trauma he caused her.
Just as he begins to gasp for air, Aurora stops the vortex, once more causing the man to crash down to the desert sand. She grabs Colcord by the collar and threatens him that she won’t let him get away with what he has done to her. The former Director of the Weapon X program doesn’t put up any resistance, instead he even begs to be killed and put out of his misery. Hearing this, Aurora changes her plans. She lets go of him, laughs out loud and takes to the air. Obviously she doesn’t consider him worth killing, Colcord realizes, as he lies in the sand and watches her leave, before he loses consciousness.
Days pass, and Malcolm’s once more unconscious, the cuts on his face covered by dozens of band-aids. He finally wakes up and is startled when he sees a pair of glowing eyes staring back at him. Jeffries comes in with the groceries he bought and apologizes if Bot, his helper robot, startled him. The robot, made of purple and gray metal, asks his master Jeffries if Malcolm is dead, but Jeffries replies that he is just drunk.. again. Jeffries explains to Malcolm he created Bot to help him out, and redesigned him because he was tired of the old Boxbot template. Malcolm sarcastically congratulates him and asks Jeffries if he got what he wanted. Jeffries got the supplies and got them dinner, ice cream for dessert and some nice cigars for a change. Malcolm doesn't care about that and, after quickly sifting through the bag with groceries, slaps Jeffries because he didn't get the bottles wanted.
Jeffries gets scared and, already raising his arm to protect his head, urges for Colcord to not hit him again. He didn't get the alcohol, because if Malcolm keeps drinking like this, he'll be dead within the week. Actually, Jeffries says, Colcord has done nothing but drink since he had brought them to the old, original Weapon X complex. That's Malcolm's plan, he states as he drinks an entire bottle of mouth wash, the only thing in the bag that contains some sort of alcohol. Jeffries lets his boss be and takes off with Bot.
Suddenly Wolverine appears from behind and mockingly tells Malcolm how far he has fallen. Malcolm can't believe his eyes and asks what he's doing here. Wolverine explains that he sometimes comes back here to clear his head, to remember why he's doing it all for. Malcolm asks him to leave, but Wolverine reveals that he hasn't come here to mock Malcolm, he's here to help him. Malcolm laughs, not understanding why Wolverine would ever help him. Wolverine says that he wants to help him because they now have something in common that they both hate: the Weapon X Program. After all, the old saying goes: the enemy of my enemy is my friend.
Malcolm tells Wolverine that he is a fool if he really thinks he'd ever help him, because he's the one responsible for destroying his face. Wolverine answers that revenge would be a pretty good reason for him to accept Logan’s offer of working together. He then turns away from Colcord , saying that he is obviously too scared to go back into the game. Malcolm gets angry and grabs a monkey-wrench to smash Wolverine's head in. Wolverine turns around and slashes Malcolm's weapon and knocks him down. He tells him to think it over, he'll be back in a few days. Once more Colcord passes out.
Malcolm has decided that Logan was right on one thing - he needs help. He and Bot repair a communication system, and Malcolm contacts his former superiors from Weapon X. They can't believe what they're hearing, because they presumed him to be dead. He informs them that Jackson and the others betrayed him. The superiors tell Malcolm that they know that. Malcolm's surprised, but thinks that they must have tortured them for Jackson to admit his schemes. The superiors explain that they haven't and Malcolm begins to understand; the superiors needed a new director and Jackson was appointed. Malcolm asks if things are running smoothly without him. The superiors explain they were, but recently, things have gotten a little complicated again.
Malcolm wants to help, but the superiors only laugh at him, not understanding how he could possibly help as he couldn't even keep his own army under control. The superiors order Malcolm to never bother contacting them again. The transmission being over, Malcolm doesn't understand why this is happening to him. Wolverine appears from behind, explaining that he's got nothing anymore that they could fear. So, he needs to get something and to get back into the game. Malcolm doesn’t understand, so Wolverine points Malcolm to Bot and asks whether he is blind. Looking at the redesigned robot, Colcord finally sees it resemblance to that of a Sentinel and realizes how things must be done.
Jeffries has created several Boxbots (in their old design), and has the complex running again. Malcolm congratulates him and is surprised how soon he got things working. He asks about the other project. Jeffries takes Malcolm to a separate room, where an entire new army of Sentinels await him! Malcolm thanks Jeffries for his fine work, because now he has a good chance at winning this time. Jeffries is only glad he could help.
They take an elevator to another level of the complex, where Logan is once more waiting for Colcord, asking about his progress. Malcolm explains to him that they're heading into the right direction again, with no small thanks to Wolverine. Logan laughs, because he would never figure that he'd ever thank him for anything. Wolverine and Malcolm shake hands, and proceed down the corridor.
Jeffries and Bot come out of the elevator as well. Jeffries is happy to see his boss laugh again, but only wishes he could do something about Malcolm talking to himself. After all there’s nobody here but the two of them.