The closing days of World War II...
Nick Fury and his troops enter a concentration camp which the Invaders have just freed. Fury orders his men to search the camp. After a while, he grows impatient and starts to look for a guy named Thorton. Some soldiers goofing off tell Fury that they call him "the Professor" nowadays and he's in the main building of the camp. Fury finds him and starts yelling at the Professor, who explains he was admiring the camp’s architecture. Fury doesn't care and orders the Professor to take two soldiers with him and dig deeper into the building.
The Professor reluctantly does as told, arguing with the soldiers as they go deeper. They find a complete lab, where something obviously has gone wrong. The Professor's fascinated but the two soldiers couldn't care less, though one does compare it to a Frankenstein’s laboratory. The Professor tells them it's okay and he'll search the lab himself. The soldiers don't need to hear that twice and leave. The Professor searches around and finds the journal of a Nathan Essex, which quickly peaks his interest.
Time passes...
The man known as James Howlett is outside a bar and is in the fight with some customers. James doesn't realize that he's being watched by the Professor and his co-workers, Dr. Cornelius and Dr. Hines, in their car far behind the bar. The Professor's fascinated with Logan: a man like he has never seen before. Cornelius jokes that the Professor knows more about these people than anyone and asks what the Professor calls them. Mutants, the Professor states. They named them mutants.
As the car departs the bar, Dr. Hines finds it suspicious that the Professor knows so much about this new phenomenon that the rest of them may never catch up. The Professor admits, while holding Essex' journal, that when it came to his research regarding these "creatures," fortune has always been on his side. Cornelius doesn't agree, because how many times has the Professor been passed over when he was still with those early Weapon Plus programs? It is past time that the Professor was given his own program. When Hines asks what number the programs are up to, the Professor reveals that it’s the tenth one, or "X" if you will. This said, the Professor returns Essex’s journal into a case, labeled Weapon X.
A little later, they arrive at a base and hear a man shouting, whose access to the base is denied by a guard. The Professor recognizes the man shouting: it's John Sublime. Sublime asks the Professor to make the guard let him pass. The Professor tells Sublime to relax, as Private Colcord's new because he only just arrived yesterday. Colcord apologizes for the mix-up and Sublime is allowed entry, though he continues his shouting. The Professor tells Cornelius that he doesn't care much for his new assistant. Cornelius tells the Professor that Sublime's more bark than bite and is harmless. But the Professor has serious doubts about that, as Sublime passes them in his car with an angry look on his face.
Time passes...
The Professor sits in his lab at Weapon X and gets a call from Sublime on the videoscreen. He is obviously not pleased with the call. Sublime mocks him, explaining that, though he now is with the Plus Programs, doesn't mean he's not interested anymore in his old Weapon X "friends." Sublime asks the Professor what he is working on – still not the “mutant thing” is it? When the Professor admits that they are, Sublime finds him ridiculous as they've come so much further nowaday in The World...
The Professor asks what Sublime wants. Sublime explains that they're shutting the Professor's program down. The Professor promises he’ll fight the decision, but Sublime's convinced that he'll lose. The Professor shouts that he won't just fade away, as he's still got friends in high places. Calling him an old man, Sublime tells him to face facts. Weapons XI and XII have already come and gone, and now they are working on Weapon XIII. And so, nobody cares anymore about his stupid mutant fixation project.
That's fine with the Professor, who notifies Sublime that, from now on, the Weapon X Program is officially breaking off from the Plus Programs. Sublime can only laugh at the remark and tells the Professor that his Programs shall be the death of him, going so far as to bet a Coke on it. When the Professor shuts the screen down, Sublime smiles and sarcastically wonders whether it was something he said.
Time passes...
Sublime stands alone over the Professor's grave, which only has the name of "John Doe" on it. Talking to the departed, he notes that, for the record, he likes his Coke caffeine-free with a twist of lemon. When Colcord appears from behind, Sublime tells Colcord that he’s glad he made it to their reunion. Colcord, with his scarred face, covered with a hat and scarf, tells Sublime that he can leave if he's only here to gloat at him. He adds that the Professor always has been a better man than he shall ever be. Sublime finds that ridiculous, as he already is better. The Professor has only a grave with a John Doe name on it, while he now leads the entire Plus Program. Colcord sarcastically congratulates him and moves to leave.
Quickly, Sublime holds him back and apologizes, because he knows how much the Professor meant to Colcord. He knows the Professor always looked after him and pulled some strings so that the government would keep Colcord after his "accident." Sublime makes Colcord an offer he can't refuse. Sublime knows how Colcord's life ended after the Wolverine incident, so he gives Colcord a chance to take his revenge and make it come true. Colcord's more than happy to accept.
Time passes...
Colcord’s present when Nick Fury and his S.H.I.E.L.D. troops are battling some A.I.M.-agents in a park. Unconcerned with the nearby fight scene, Colcord stands calmly on a small bridge, speaking on the phone with Sublime. Colcord thanks Sublime for the opportunity he’s been given. On the phone, Sublime replies that he only hopes that their deal still stands, so that everybody gets what he wants. Sublime states that the only trouble he sees is whatever will they call it. Colcord's already thought about that and has decided to name it “Neverland.” Sublime likes the idea and asks if Colcord has thoughts about who shall be in his "work force." Colcord takes out a notebook which reveals possible mutant candidates. However, Colcord’s still wondering who his second-in-command should be.
The fight with A.I.M. escalates when the next to last A.I.M.-agent is killed by Fury. The final agent, however, is holding a little girl hostage and refuses to let the kid go. Fury orders the A.I.M.-agent to drop his weapons. The agent laughs and takes off his mask and reveals that he is the weapon: he's a mutant. Fury orders his men to drop their weapons. They do and the mutant laughs, until he is killed bya single shot from agent Brent Jackson from behind. Fury yells at Jackson because he could have gotten the girl killed. Jackson says that he didn't. Fury can either write him up, or thank him for ridding the world of another “stinkin’ mutie.” As they continue to argue, Colcord calls Sublime back, saying that he has found his second-in-command.
Now...
Agent Zero walks through the deserted Weapon X base. He switches on a computer and, all at once, at every computer screen, the word "Roanoke" appears.
Now...
Wolverine enters the deserted Neverland. He unsheathes his claws and can't believe his own eyes. He lights up a lighter for a better look and sees on the wall the word "Roanoke."
Now...
Fantomex, who’s at a graveyard, digs up the grave of John Sublime but finds the coffin is empty. Fantomex, however, is not to surprised, stating to himself that he might have known. As he walks away, Fantomex leaves behind the open and unearthed coffin, which contains only a card with the word “Roanoke” written upon it.
