Several days later, while the X-Men were on a mission, Jean Grey was captured. Weapon X abandoned the team and infiltrated Mister Sinister’s laboratories alone, successfully freeing her. Inside, he confronted Prelate Scott Summers, and the two engaged in a brutal battle. Weapon X tore out one of Summers’ eyes, while Summers retaliated by destroying Logan’s hand with an optic blast. Refusing to return to the X-Men, Logan and Jean chose to operate independently. After months of guerrilla warfare, they were contacted by Sinister, who revealed Apocalypse’s plan to launch an assault on humanity in Europe. Logan and Jean relayed this intelligence to the Human High Council, only to discover that the Council intended to launch nuclear missiles at America in an attempt to stop Apocalypse.

Jean left to warn the United States, while Weapon X remained behind. The Human Council was soon attacked by genetically altered humans created by Mikhail. Weapon X defeated them, but not before they sabotaged the Sentinels’ guidance systems. Logan then traveled to Wundagore Mountain to retrieve the mutant Gateway, whose teleportation abilities were needed to relocate the Sentinel fleet and the nuclear warheads. Once airborne, the fleet was attacked by another group of altered humans led by Donald Pierce. Weapon X killed Pierce by extending the claws that still protruded from his mutilated, handless arm.

Upon reaching America, Logan parachuted into New York City in search of Jean. He arrived only to witness her death, killed by a plasma blast from Prelate Alex Summers. Consumed by rage, Weapon X slaughtered Jean’s murderer and remained beside her body as the nuclear warheads descended upon the country. Somehow, the missiles failed. In the chaos that followed, Weapon X vanished—and has not been seen since.