After having his telepathic affair with Emma Frost discovered by his wife Jean Grey, Cyclops leaves the Xavier Institute for Higher Learning and the X-Men. Not knowing what to do, he goes to the Hellfire Club to watch the exotic dancers and get drunk. What he doesn't expect to find there is Wolverine. Wolverine invites him to do some "serious drinking", and turns it into a wager. If Scott can out-drink Wolverine then he can get back to doing whatever he wanted to do. If Wolverine wins Scott needs to help him out with a mission. Wolverine had arrived with Fantomex, who had promised to help him uncover the truth behind their origin and the Weapon Plus program. Wolverine tracked down Scott to help them. Scott lost the wager and passes out.
Cyclops, Wolverine, and Fantomex arrive to Weapon Plus's The World to find that someone had already been there before them. The remains of a team of A.I.M agents is all over the place and the only remaining member is not in a position to tell them much. Fantomex deduces that Ultimaton (Weapon XV) had killed the agents. He explains that within The World time is artificial, and can be sped up, slowed down, or stopped completely. The inhabitants of The World were engineered from biological creatures as well as micro-sentinel technology. Speeding up time within The World and regular Gamma radiation bombardment allowed Weapon Plus to artificially stimulate evolution within the inhabitants. Their goal was to create super-human soldiers to fight in the pending war between humanity and mutant kind.
Fantomex pauses time within The World and they venture inside the dome to locate Weapon IV. It has not been long on the outside since Fantomex escaped The World, but inside the dome generations had passed. Within the world they saw World Police Cars driven by whale brains, and massive destruction. All of the other inhabitants of the world were killed by Weapon XV. The doors to the world slam shut as the last surviving agent of the A.I.M. raid turns time within The World back on, releasing Weapon XV from stasis. The three are able to find XV quickly, but are of little use against him. Fantomex signals for E.V.A to regain control of The World from the A.I.M. agent, but when she gets to the controls she realizes that Weapon XV has locked her out. After beating Wolverine, Cyclops, and Fantomex in combat, Weapon XV smashes out of The World, freeing himself.
Within E.V.A. they tracked Ultimaton to a nearly completed space-station orbiting around the Earth. Within they found the records of the Weapon Plus program, as well as its plans. The Super-Sentinels that were Weapon XII through XV were designed to rid the world of mutants. Within the station EVA was captured by Weapon Plus, and killed. Wolverine had read the files about himself and those that came before him, learning that the Weapon Plus program started back in World War II with Captain America: Weapon I. Wolverine also discovered that there was a traitor within the mansion, someone sent to infiltrate them. Ultimaton found Wolverine and before he could do anything Wolverine triggered the auto-destruct for the station. Cyclops and Fantomex are able to escape in one of the planes.
Professor X uses Cerebro to find Wolverine is still in space. The explosion had thrown them into a nearby asteroid near the course of the satellite. Jean Grey takes one of the X-Planes to rescue Logan. She finds him destroying Weapon XV, and recognizes that the asteroid they are on is no ordinary satellite, it is Magneto's former base Asteroid M.
Murder at the Mansion - The events that took place before Assault on Weapon Plus, including the attempt on Emma Frost's life.
Planet X - The events of Assault on Weapon Plus are continued through the Planet X story-arc.