Wolverine, all sweaty, sits against a tree with his claws open. He looks straight ahead and there’s blood all over the street roads, and lots of people… killed! At the back of a house, Cornelius and the Professor look at their weapon. Cornelius asks if the Professor’s satisfied now, now that they’ve seen how far they could take Logan. The Professor tells Cornelius to keep his sanctimonious tone to himself, as this experiment was necessary, whether they’d liked it or not. The Program needed to determine Experiment X’s abilities. Cornelius asks if that means to slaughter innocent men, women and and children. While Cornelius and the Professor walk through Roanoke, soldiers gather the bodies and put them all together.
The Professor finds it a shame that, once again, Cornelius fails to see the bigger picture. Cornelius needs to think beyond the dead here in Roanoke; he needs to think Moscow, or Tehran. The Professor and Cornelius watch the soldiers burn up the corpses and put the whole town on fire. The Professor imagines that one day, they can drop their Weapon X or somebody like him into the cities of America’s greatest enemies, when the need arises, with zero risk to their own troops. The Professor agrees with Cornelius that today they did take 116 lives, but potentially saved so many more. Cornelius isn’t much relieved and asks how the Professor plans to keep their little mini-holocaust hidden.
The Professor explains that the selection process while coosing Roanoke as their test site went far beyoned the novelty of its name. Roanoke is small and self-contained, so it will not be so unbelievable that all its denizens perished in a horrible fire. With this, they have also wiped out all evidence of Roanoke from the face of the Earth, and it will be as if they never existed at all. Cornelius can’t believe how the Professor is able to sleep at nights. They walk pass Logan, still sitting and recovering, and the Professor jokes that he sleeps with two pillows and a quilt sewn by his late Aunt Trudie.
Wolverine now remembers all these events and has revealed them to Fantomex and Agent Zero. Wolverine has learned this from the files he saw at the World. Now, Wolverine finally knows that he is the killer he always feared he was. Fantomex finds that nonsense, as they both known that Wolverine couldn’t help what the Weapon X Program controlled him to do. Zero agrees, because all three of them know the horrors that the Program is capable of. Wolverine brings an angry look on his face and asks Fantomex who the guy is he brought with him.
Fantomex introduces Zero to Logan, but he knows who he is. Wolverine unsheathes his claws open and wants to know what one of Weapon X’s top employees is doing here, as this could all very well be some sort of mind game of Weapon X. Zero can’t believe it. Zero tries to defend himself, not wanting to shoot Logan, but, before they can fight, holds Fantomex them back. Fantomex tells Logan that he’s got it all wrong, as he knows a thing or two about lying, and Zero is telling the truth when he says that he is no longer working for the Program. Wolverine still doesn’t trust him and will be keeping an eye on him. As for a guy with no scent, Wolverine finds something not right about him. As Wolverine leaves and enters the woods, Zero jokes how an intense little guy Wolverine is.
Fantomex says that most people come to that conclusion when first meeting Wolverine. And, after all, this is Zero’s “first” meeting with Wolverine. Zero remains silent for a while and says it is, following Wolverine into the woods. Fantomex, not convinced, follows as well. They find Wolverine nearby a broken tree trunk and asks what he’s doing. Wolverine find this trunk right before they showed up and, on the trunk, stands the word “Croatoan,” and in the second “O” is a button made. Fantomex finds this interesting. Wolverine, too, and he has been wondering whether to push it or not. Zero bets that E.V.A. could analyze this thing, if she weren’t out scouting the area. Fantomex sighs, finding it a blessing that Zero doesn’t talk much. They don’t need E.V.A. and it’s been obvious that they’ve been led here for a reason, and the reason will only become clear when they push the button. The three mutants look at each other and Wolverine has enough of it, so he decides to push the button anyhow. As he does, the ground starts to shake.
A large video-screen shows up in the ground, revealing a man wearing a mask. The man greets them and, as he takes his mask off, the man is revealed to be none other than John Sublime! Fantomex recognizes Sublime, but isn’t surprised to see him, as despicable secret program directors are getting harder and harder to kill these days, as it would seem. Sublime sacracstically says he’s glad to see Fantomex again as well, and of course he shouldn’t be surprised, as one can’t reach the top of the Weapon Plus Program without outsmarting an assassination attempt or twelve. But, finds Sublime, that lies all in the past and they should be dealing with the here and now.
After all, they’ve dwelt enough in their past for one day, as Sublime points to Logan. Sublime jokes how a touching scene he found it, hearing him telling his story. Sublime thinks it’s clear now that they let Wolverine see those files at the World. They wanted him to unrepress those events of his life and ultimately bring him back to the “scene of the crime.” But Sublime wonders why Agent Zero is here. Sublime belives that Zero wants to know if he’s searching for his Program he now appears to be free of, and making sure that they’re really gone for good. Sublime tells Fantomex that he was like a son to him, so much so that Fantomex had to find out if his “father” was still alive and kicking. Fantomex angrily takes out his gun and says he won’t be much longer if he’s got a say on it.
Wolverine holds Fantomex up. Wolverine tells Sublime that he’s got him now, and wants to know why he brought them all here. Sublime says it’s because they are at war. Sublime shows pictures of the Weapon X agents, who apparently know that they’e gotten too big for their britches. Sublime reveals that agreements were broken, double-crosses were crossed and assassinations were attempted. And now it seems that Weapon X wants to take a shot at Sublime’s Weapon Plus, which suits him just fine. Sublime finds this the reason to believe that Weapon X have packed up their various operations and have moved underground, so they are harder to find.
Sublime has something to say about that, as they are taking a page from Weapon X’s book even as they speak now. After years of service to the Plus Programs, this installation is now officially closed. The video-screen opens, and Sublime sarcastically says that this is a going –away party. And they three have been invited. Sublime says that they’ve discovered that one of the mutants belongs to the Weapon X Program body and soul. Sublime doesn’t reveal who it is, and he’s uncertain if the person himself is even aware of it. But instead of letting the person figure it out, Sublime rather kills them all with his precious U-Men. Various U-Men show up from the undergrounds and Sublime leaves from the video-screen, saying he’s got some packing to do himself.
Wolverine, Fantomex and Zero guard each other, trying to figure out what to do. Wolverine says he’s going to keep killing U-Men until he drops dead. Zero asks what’s going to happen if they make it out alive. Angrily, Wolverine says that they are going to have their talk then. This sounds good to Zero, so the three mutants unleash their power and begin fighting the U-Men. They soon find themselves outnumbered and caught, but, when it seems to be the end for them, E.V.A. arrives on the scene and shoots her way through the U-Men. Fantomex tells her she’s a little late, on which E.V.A. replies that there’s just no pleasing some men. Fantomex and Zero fight their way to E.V.A. and climb her escape ladder, back inside. Wolverine soon follows, but he sees Sublime leaving in a plane.
Fantomex tries to hold him, but Wolverine unsheathes his claws again and jumps in full rage at Sublime. Wolverine shreds the window from Sublime’s plane. Sublime asks Logan if he never quits, to which he replies no. Sublime smiles, as his U-Men appear to not quit ever. A flying U-Men shows up, but Wolverine jumps at it and kills it with his claws. The U-Men drops on Sublime’s plane, breaking it completly, and Wolverine shreds his way through it as well. The plane takes a heavy crash, but Sublime lives through it. Wolverine stands triumphantically over Sublime, who panics a little. Sublime tries to calm Wolverine down, wanting to make an agreement, as there is still much he can show him. Wolverine wouldn’t know what that is, because now he knows everything he needs to know: he’s a killer.
Wolverine grabs Sublime by the throat, saying that he’s going to kill him now. But before he can, Fantomex shows up with E.V.A. and grabs Wolverine on board. Wolverine angrily asks what Fantomex thinks he’s doing. Fantomex tries to explain that, seeing that Wolverine was about to be swarmed by bloodthirsty U-Men, he rescued his life. Wolverine tells Fantomex that now would b a good time to have their talk. The U-Men want to follow the mutants, but Sublime knows they’d never catch him, so he lets them go. Besides, he has always a plan B to go to. Weapon X may have made their move against one of those three men already but, after today, so has he.
A grassfield is burning. E.V.A. lies in the field, destroyed and in flames. Beneath her lies Fantomex, badly injured and not moving. Agent Zero and Wolverine are nowhere to be seen…