After a night of drinking, Wolverine is attacked by several men (Wolverine #47). He was getting into his car when several men attacked him. They tried to use a stun gun to no effect, and they eventually shot Logan 5 times and beaten up until he was unconscious. He was then taken to a seceret nuclear plant in Alberta Canada where the Project X took place.

Logan was kidnapped by agents of the Weapon X Program (Marvel Comics Presents #72-84), an outgrowth of the Team X Project, shaved clean and free-floated in a tube. Needles and probes riddle his body.

At this time, in contrast to its previous ties to the CIA and others, the Weapon X Program is apparently not directly sponsored by any government agency, although some of its employees are deceived into believing otherwise; it will later be absorbed into Canada's Department H, whose head, James Hudson, also comes into possession of notes on Lord Dark Wind's bonding process.

The Professor was the head of the Weapon X project and was alleged to have previously worked on the Team X Project (Wolverine #64) during Logan's tenure. Carol Hines was a former N.A.S.A. employee who was recruited into the Weapon X project by the mysterious Professor. With Doctor Cornelius they begin the process of bonding adamantium to Logan's bones.

This adamantium bonding process was apparently stolen from the Japanese scientist known as Lord Dark Wind (Alpha Flight #34). It is known that James Hudson had the Lord Dark Winds records a year before he found Wolverine (after escaping from this Weapon X project). How he got them is unknown. His wife Heather once wondered if James had planned their surprise meeting of Wolverine (Alpha Flight #34).

Work in this field has also been done by American scientist Dr. Ronald Rankin (Marvel Comics Presents #61), whose son Calvin will, years later, develop superhuman powers and become known as the Mimic; whether or not Rankin is directly involved in the experiment upon Logan is unknown.

Years later, upon being confronted by his fellow X-Man Archangel (Uncanny X-Men #242) after the latter has been surgically altered by the immortal mutant Apocalypse (Wolverine: The Jungle Adventure), Logan will sense something "familiar - pain" in Archangel's scent (Uncanny X-Men #242), suggesting that technology created by Apocalypse was also involved in Logan's own transformation.

The Professor and his staff seemed unaware of Logan's mutant nature. It's Hines who notices that within 40 minutes of the experiment's start, that Logan's hair has almost completely grown back and whatever injuries he sustained at the hands of his kidnappers barely register in the readings.

Logan's claws manifest for what is apparently the first time in his life.

The Professor tells Cornelius that Logan is ready to be trained as a killing machine. "Shot, stabbed and beaten in the course of duty - recklessly seeking the honor of dying for his country. How pitfully desperate he must have become. Yes. Indeed. But now his demon is free-released by the intervention of experiment-x. Thus the double id is supplanted by the super ego and all of Logan's primal instincts are focused and resolved."

Logan tries to break free but is gassed, on the order of the Professor.

Cornelius is horrified by this action. "Isn't he still human in some way?"

The Professor answers, "Your earlier description was more apt. A mindless, murdering animal."

Cornelius who will control Weapon X via a series of wires and controls sewn into Logan's body. Using virtual reality mixed with actual fight scenarios, Logan is brain-washed into becoming a mindless killer.

Aldo Ferro (Psi-Borg) was offered to used his psychic powers to implant false memories, in return for Wolverine's DNA: he wanted to slow down is own aging; he never got it (Wolverine #64).

Eventually, Logan believes that he kills everyone at the complex including Cornelius and flees the lab into the wilds of the Buffalo Woods Park in Northern Alberta.

After Wolverine escaped, Hines disappeared.

Driven into savagery by the experiment, Logan wanders the forests of the Canadian Rockies for months (X-Men: Heroes for Hope), living in a feral state, ironically, not far from the place of his birth; it will be many years before he fully regains his memories of his earlier life.

During this period, Logan saves the life of a creature known as a Hunter in Darkness (Wolverine #34), one of a race of feral beings apparently mystical in origin. A psychic link of some sort (Wolverine #84) is established between the two, to resurface in later years. On occasion, Logan's human personality surfaces to the extent that, years later, he is able to recall pleasant experiences in these woods (Marvel Comics Presents #130). Years after this experience, Logan's memories of much of his past will remain clouded as a result of the Weapon X experiment, and it is possible that he received additional false memories during the procedure as well.