James Hudson was invited by the Canadian Prime Minister to help create Department H, a top secret research and development agency within the Canadian Ministry of Defense, whose facilities Logan broke into mere months ago and which will, ironically, be combined with the Weapon X Program within months more; however, despite speculation to the contrary, Hudson played no direct role in Logan's experiment. At this time, Department H is conducting research in several fields of superhuman study but as yet has no clear direction, and Logan is one of Hudson's first recruits for the operation.

He and Heather McNeil became engaged, who was still not yet twenty. McNeil also became a member of Department H, serving as Hudson's secretary. Heather McNeil glimpsed reports on James Hudson's desk of a process to bond adamantium to bone, translated from the Japanese. However she dismissed the reports from her mind, and did not recall them again for years. (Alpha Flight #34)

When James had married Heather McNeil, the pressures of work had forced them to repeatedly postpone their honeymoon, until now. Their were spending their honeymoon in the Wood Buffalo National Park in the Rockies so they could go hunting (Alpha Flight #33; Uncanny X-Men #140; Alpha Flight vol2 #3).

Suddenly, they were attacked by something that seemed more beast than man, utterly savage, apparantly incapable of human speech. If not for the remnants of clothing he wore, one might believe that the beast-man had been raised by animals - wolves, perhaps, like poeple of ancient legends - and had never seen another human being before. The wild man might have torn apart James Hudson, but Heather overcame her terror enough to fire her rifle at the savage. The gunshot would have killed any normal man on the spot.

Amazed that the man was still alive, they brought him back to their cabin, and tied him down to the bed. Not knowing about Logan's healing factor, they thought him to be completely helpess. Thinking the unconscious man could not harm Heather, James left her alone while he went to find medical supplies. Much later, Heather will wonder if James had known that they would encounter Logan in the park, and if he had left the two of them alone for his own machiavellian reasons.

Unseen by Heather, Logan regained consciousness. Acting by sheer instinct, he used his claws to cut his bonds.Then, suddenly, he took Heather by surprise and again, acting instinctively, unsheathed his claws in full view of her. But Heather was not nearly as shoched by this sight as Logan was himself. It was as if he had never seen his claws before. As far as it's known, he never has. He was struck with absolute terror at the sight of the strange unnatural things protruding from within his own hands. Somehow, though Logan had lost his ability to think clearly and had descended to an animalistic madness, he still could not believe this. His initial panic and horror soon passed, and the "wild man" sunk into a deep, unnaturally silent melancholy. It was the reaction not of an animal, but of a man tormented by life. Watching, Heather Hudson found herself overwhelmed with sympathy for the man who had twie tried now to kill her. He no longer reminded her of a beast, but, strangely enough, of a child needing her comfort and support.

James and Heather Hudson return him to Canadian society and are instrumental in his eventual recovery. Slowly, Logan recovered his humanity, and his ability to walk. He lives with the Hudsons for some time, and he is present when Heather Hudson's parents (Alpha Flight #47), objecting to their daughter's elopement, confront her at the Hudson residence.

Logan is also present when the Hudsons renew their vows in a Catholic ceremony months after their first, less formal marriage, an event which is temporarily delayed when a Cosmic Ray Collector developed by Department H overloads (Alpha Flight #-1). In the course of this disaster, the retired super-hero called Chinook is horribly mutated and driven mad by the cosmic rays; Logan and Hudson, the latter using a prototype of the battlesuit he will later wear as Guardian, halt Chinook's rampage, apparently at the cost of his life.

Logan and the Hudsons are assisted on this occasion by Eugene Judd, whom Logan, still suffering from memory loss, does not recognize as his near-adversary of years before; following Logan's resignation in later years, Judd will join Department H under the name "Puck."

Early during this period, Logan, seeking more information on the experiment to which he was subjected, travels to the US, where he consults adamantium expert Dr. Myron MacLain (Wolverine #-1); Logan is flown on this occasion by pilot Ben Grimm, who will in less than three years be transformed by cosmic rays into the superhuman powerhouse known as the Thing.

Following a consultation with MacLain, Logan is targeted both by Sabretooth, although whether on behalf of the Hellfire Club or other parties is unclear, and by HYDRA, under the command of Silver Fox; he is aided against his assailants by several former allies: CIA agent Nick Fury; Carol Danvers, working alongside Fury with the CIA on this occasion; and Natasha Romanova, who has gone to work for the USSR under the codename of the Black Widow. Apparently, this marks Romanova's first meeting with Logan since her childhood, for she does not appear to recognize him (although this could be subterfuge on her part). Logan, still suffering from memory loss, recognizes none of his former allies. Inexplicably, Danvers appears to have no memories of her previous work with Logan, either; whether this is subterfuge on her part or an indication that she, too, has undergone memory alteration (either by her own government employees upon approaching Senator Kelly or, perhaps, by agents of the Hellfire Club in the aftermath of her previous adventure with Logan) remains unknown.

Following his recovery, Logan, this time under the supervision of Department H, again goes to work for Canadian Intelligence, where he is given "dirty, brutal, necessary assignments no one else would touch" (Uncanny X-Men #140). In this new phase of his life as an agent of the Canadian government, Logan serves primarily in Siberia and the Western Pacific, notably the Pacific Rim of Asia and the islands along that coast, including his old stomping grounds of Japan. Logan masters various languages of the Orient during this period (Classic X-Men #10, Wolverine Saga #1), and he is also specifically taught Russian (Wolverine and Nick Fury: Scorpio Rising, Uncanny X-Men #268), although he never achieves the same level of skill in it as in other languages.

Years later, Logan will note that, as both a wartime soldier and a secret agent, he earned many medals and commendations (Uncanny X-Men #140); since his full memories of his time with Team X will not re-surface until some time after he makes this remark, it is presumably during this period that he earns some of these commendations. During the first few years of this period of his Canadian service, he will use only the alias "Weapon X," perhaps in subconscious recall of his Team X days. Having already attained the ranks of Major and Commander in other agencies, Logan eventually attains the rank of Captain in the Canadian Armed Forces during this period (Uncanny X-Men #120, 158).

One of Logan's first missions as Weapon X takes him to Iraq (Wolverine #9). Certain Iraqi militants had hired terrorists to seize the American embassy there and hold everyone within as hostages. There were some Canadian citizens in the embassy as well when it was captured. Hence, when the American government sent in the Delta Force (a special team of US government operatives) to recapture the embassy, the Canadian government sent Weapon X along with them. During the American storming of the embassy, Logan found a Canadian nun who had been mortally wounded in the crossfire. As she died, she told him how one of the mercenaries, named Bruno Malone, had psychologically and sexually abused her during her captivity. Her dying wish was that Malone should be made to suffer for what he had done. Logan was enraged that Malone had broken the spirit of this woman of peace to such a degree that she had died asking for vengeance. Logan is prepared to act upon this vow of vengeance immediately, but apparently his new responsibilities as an agent of Department H prevent him from doing so, since he will later claim that he "got...busy" immediately following the Iraqi mission. Logan does not forget his vow, however, and he will fulfill it years later.

Still suffering from memory loss and recurring berserker rages, Logan goes through a period of adjustment to his new role, and it may be during this period that he incurs several debts to fellow Canadian Intelligence agent Jack Oonuk (Punisher War Zone #19), who possibly covers for him with the authorities.

On one mission for the Canadian government, Logan spends four months in Hong Kong (Wolverine #119-121), a place that he has presumably visited often in the past, where he finds himself in conflict with the organized crime unit known as the Triads; he also encounters the noted assassin McLeish, known as the White Ghost, whom he will meet again years later. It may also be during this period that Logan first meets a woman named Linn Chow (Marvel Comics Presents #40), to whose aid he will go in later years.