Logan trained Magneto's newer recruits, including Kitty Pryde. Unbeknown to the rest of the X-Men, Magneto had asked Weapon X to train the girl as an assassin. Weapon X taught Shadowcat everything he knew and even crafted a pair of claws for her with Magneto's help.
Days later the X-Men were on a mission when Jean Grey was captured. Logan begged Magneto to send his team to save Jean but he refused. Weapon X left the team and went on his own. He infiltrated the labs of Apocalypse's Horseman, Sinister, and was able to free Jean. Inside he encountered Prelate Scott Summers and the two fought ferociously. Weapon X gouged out one of Summers' eyes and the Prelate blew off Logan's hand with an optic blast.
Not willing to return to the X-Men, Logan and Jean worked on their own. After months of guerrilla warfare, they were contacted by Sinister who revealed Apocalypse's plan to attack the humans in Europe. Logan and Jean delivered this information to the Human High Council, learning of the Council's plan to launch nuclear missiles on America to stop Apocalypse.
Uncomfortable with leaving the X-Men and the humans of America to nuclear obliteration, Jean went to warn them. Weapon X stayed behind with the Human Council and reunited with an old flame, Mariko Yashida. The Human Council was attacked by a group of genetically altered humans created by Mikhail. Weapon X defeated them but not before they destroyed the guidance system of the Sentinels. Weapon X traveled to Wundagore Mountain and retrieved the man known as Gateway. The aboriginal mutant would be able to teleport the Sentinel fleet and nuclear missiles with his mutant powers.
The fleet took off and was attacked by another group of altered humans led by Donald Pierce. Weapon X defeated him by extending the claws that still resided in his handless arm. When Logan reached America, he parachuted down to New York City looking for Jean. He arrived to see her murdered by a plasma blast from Prelate Alex Summers. Enraged, Weapon X murdered Jean's killer and sat by his lover's side as the nuclear warheads fell on America. Somehow, the missiles failed. Weapon X disappeared in the chaos that ensued and has not been seen since.