As part of another early mission for Department H, Logan joins forces with Ben Grimm (during Grimm's days as a test pilot for the U.S. Air Force) and Carol Danvers on a special mission into Russian territory, under the orders of Colonel Nick Fury and with information provided by industrialist Tony Stark, who will within a few years begin a career as Iron Man (Grimm and Logan #1-3).

Logan, Ben Grimm and Carol Danvers, USAF, were shot down and captured by an elite Soviet strike force as project Red Storm was unveiled, and had to find a way to escape - that didn't involve killing each other! Why were they seemingly betrayed? And why did the Black Widow seem to know their next moves?

On this occasion, for reasons which remain unclear, Fury deliberately pretends to have no previous experience with Logan, and Danvers continues to demonstrate no recollection of her own work with him. In the course of this mission, Logan refrains from using his adamantium claws, although whether this is due to inexperience, subterfuge, or simple whim is uncertain.

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

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.

Three years into Hudson's directorship of Department H, over two years after Logan was found by the Hudsons, the Fantastic Four, the first verified public team of super-heroes in decades, debuts to worldwide acclaim. Inspired by this, Hudson elects to orient Department H toward the formation of a government-sponsored Canadian super-team that will operate in the public eye (Alpha Flight vol2 #3). His first choice for a member was Logan (Alpha Flight #52).

In preparation for his career as a publicly-known super-hero, Logan is outfitted with a distinctive yellow-and-blue costume.

Logan, contemplating the wisdom of this new career, returns to Madripoor, the site of some of his earliest heroic activities, for what may be the first time since his freelance years and spends some months there, where he is reunited with his old friend Seraph (Wolverine #126). Seraph introduces Logan to another pupil of hers, Viper, who is, as Logan once was, a freelance espionage agent, although, presumably unknown to the others, Viper's activities are usually terroristic in nature, and, by coincidence, among her clientele is HYDRA, in whose ranks she will eventually rise high. Like Logan and Seraph, Viper, born prior to World War II, ages very slowly; in Viper's case, this is due to a pact she made with the Elder God known as Chthon decades ago, during her youth in war-torn Europe.

During this time, Logan and Viper assist Seraph in her ongoing activities against the Hand, and this appears to be the earliest instance in which Logan wears his yellow-and-blue costume in battle; on one occasion, Seraph and Viper risk their lives to rescue Logan from Sabretooth, who may have been working with the Hand at this time. It is possible that Seraph is in fact slain during these events, but this is as yet unclear. This incident marks Logan's last visit to Madripoor until recent years (Marvel Comics Presents #1).

As for Viper, she and Logan will periodically clash after he has joined the X-Men, until the two eventually marry for the sake of maintaining peace between criminal factions.

Moved by Seraph's example of heroism, Logan returns to Canada to undergo training to become part of this new team, which eventually became known as Alpha Flight. Hudson nominates Logan for the eventual leadership of this team, which, in its early stages of development, is known as "the Flight."

Trying at first to keep information about their special operative a secret, the Department gave him the code name of "Weapon X." But Logan preferred to refer to himself as Wolverine.

To better prepare for his eventual role as Flight leader, the goverment spent millions of dollars in training Logan for this new role. Much of this money went toward psychollogically reconditioning Logan (Uncanny X-Men #96) in an attempt to eliminate his beserker tendencies. Drugs and hypno-therapy were among the means used to try to "cure" Logan. By his own later testimony, the treatment he received went a long way toward entirely suppressing his inner rages. But they didn't eliminate them. As a part of this therapy, which he will intermittently receive throughout his career with Department H, Logan apparently spends time in asylums in the United States (Marvel Comics Presents #44); at least one of these facilities is operated as part of an American prison (Marvel Team-Up #117), which Logan will later claim houses "the biggest bunch of hardened criminals you could find...the lowest of the low."

Despite Hudson's plans for a Canadian super-team, at this time Logan remains his only candidate (Alpha Flight #52), and Logan lingers in Canada for months while Hudson continues his search for other suitable candidates. While on leave following his Madripoor exploits, Logan is recalled to duty to confront D'Von Kray, a Canaanite warrior from the fortieth century in pursuit of the mutant time-traveller known as Cable (Wolverine/Cable: Guts and Glory; New Mutants #94), who himself has only recently arrived in the twentieth century. Wearing his yellow-and-blue costume on a Canada-based mission for the first time, Logan battles and defeats Kray, who is taken into custody by Department H, only to escape soon afterward and track Cable to New York City in the United States, with Logan in pursuit. Following Kray's defeat and recapture, Logan and Cable briefly meet for the first time; despite their shared efforts in battling Kray, the meeting is not a friendly one.

Some time after this, Cable becomes active as a mercenary and leader of the team of operatives known as the Wild Pack or the Six Pack, and, over the next few years, he and Logan periodically re-encounter each other and develop a less-than-friendly rivalry, although they will later work together under the aegis of the X-Men.

Still active in Canada at this point as an agent of Canadian Special Services, Logan is partnered with Colonel Rick Stoner (Fury one-shot) of the CIA to retrieve a prototype of Hudson's original Guardian armor, stolen from the US/Canadian research facility Am/Can by HYDRA; although Hudson used a reconstruction of this prototype in his earlier adventure against Chinook and will later use a far more advanced model, presumably this earlier model remained in Am/Can's custody due to legal technicalities. On this occasion, Logan, apparently in order to distance his espionage efforts from his role as super-hero, does not wear his costume into battle and refrains from using his claws, instead relying on a large dagger in battle, much as he did during World War II. Shortly after this, Stoner is recruited as head of the newly formed international espionage agency known as SHIELD; some months later, Stoner suffers fatal wounds in a battle with HYDRA, and the SHIELD directorship falls to Nick Fury.

Under pressure to produce additional super-agents, Hudson subjects a convicted murderer, offered amnesty, to an experimental process designed to manifest any latent superhuman powers. Logan is leery of the idea, and he warns Hudson that the convict, who will later become known as Bedlam (Alpha Flight #52), may prove uncontrollable; he will be proven right some years later.

Disturbed by Hudson's revelation, Logan elects to return to his intelligence operations, although he will remain on call for the Flight as necessary; over the next few months, Hudson, having placed his experiments with Bedlam temporarily on hold, recruits nearly a half-dozen other superhumans as potential Flight members, whom Logan trains in combat at select intervals.

While dividing his time between the Flight and espionage, Logan shares few details of the latter work with the Hudsons; it is only years after this period that Heather Hudson even learns that Logan speaks Japanese (Alpha Flight #34).

As an operative of the Canadian Secret Service, Logan cooperates with intelligence agents from many other nations. Foremost among these is his old friend Carol Danvers, still with USAF Intelligence; Logan works frequently with both Danvers and her partner in USAFI, Michael Rossi (Uncanny X-Men #154), on "some pretty hairy capers," some of them in Saigon, Vietnam, and Tokyo, Japan, where Danvers teaches Logan how to play poker (Marvel Fanfare #24).

At some point during these years, Logan and Danvers become romantically involved (Uncanny X-Men #154; Marvel Fanfare #24). When working with Logan, Danvers uses the codename "Ace," while Logan resurrects his former alias of "Patch" (Uncanny X-Men #238). On occasion, Danvers also calls Logan by the affectionate nickname of "Wildboy" (Uncanny X-Men #236). It is not known if, during this time, either Logan or Danvers ever regain their memories of their previous exploits together.

While in Japan, Logan also works extensively with Asano Kimura (Wolverine Limited Series #1) of the Japanese Secret Service, whom he may have met decades earlier as a youth. Kimura develops a great respect for Logan, whom he will later characterize as "more truly Japanese than any westerner I have ever known." During his time in Japan, Logan occasionally observes Japanese government efforts against various gigantic monstrous creatures (Uncanny X-Men #181; Godzilla #2), many of them prehistoric life-forms released from natural suspended animation, which periodically attack populated areas and which much of the rest of the world mistakenly believes to be fictitious. It is not known if Logan ever directly participates in such operations.

In Japan, Logan, pleased to be able to renew old ties, continues his samurai studies under Ogun and others; years later, martial artist Yuji Watanabe (Marvel Comics Presents #67) will claim that he and Logan have "several mutual acquaintances," although the two do not meet during these years.

It may also be during this time that Logan renews his acquaintance with Gomurr the Ancient; other acquaintances of Logan's from these years, fellow intelligence agents, include Irish Interpol agent Sean Cassidy (Wolverine #141), Clive Reston of the British MI-6 (X-Men #62), and Jack Bascomb of the American CIA (Wolverine #19). As an agent of the Canadian Special Intelligence Service, Logan's direct CIA liaison is Henry Peter Gyrich (Uncanny X-Men #228), who will later go on to be involved in the US government's mutant-control operation Project: Wideawake. Presumably Logan renews his friendship with Nick Fury during this period as well.

At times, Logan accompanies Danvers and Rossi to the US. He visits Chelsea, NY (Classic X-Men #10), on occasion, and for a time, under the aegis of the Canadian military, he is stationed at Valhalla Base (Uncanny X-Men #94-95), part of the NORAD defense system; at some point during this stage of his life, Logan, visiting the Hudsons in Canada (Uncanny X-Men #147), suffers from a berserker rage and nearly kills them, and this event may take place during this period, since he is wearing a military uniform at the time.

Another American colleague of Logan's, whom he may have met prior to this period, is an unnamed superhuman, who, like Logan, holds the rank of captain; years later, when this man has lost his super-powers and fathered a daughter who manifests powerful mutant abilities, Logan will arrange false identities for them in Kansas, where they will live under the name "Beck" (Marvel Comics Presents #50). According to one account, during these years Logan even has a longterm residence in San Francisco, CA (Deathblow and Wolverine #1-2), which he shares with a young woman named Sung Li; according to this account, Sung Li's relationship with Logan is ultimately intended to manipulate him into destroying a mystic artifact, which he does in the company of another adventurer.

It may also be during this period that Logan undertakes an assignment in Houston, TX (Havok and Wolverine #1), in which at least some intelligence agencies will later believe him to have been killed. About a decade later, an American intelligence operative named Roberts (Marvel Comics Presents #109) will claim to have worked with Logan in "Frank's division" on a mission in which they "shared the trenches"; however, Logan will have no recollection of this mission, and since Roberts is, like Logan, a victim of memory implants, in his case by the US government operation known only as the Project (which may or may not be identical to the Team X Project), it is unclear whether or not this claim is based in reality.

Some months after the debut of the American super-team known as the Avengers, Logan recruits Canadian Detective Sean Benard for the Flight (Alpha Flight Special #1); Benard is assigned the use of the Guardian armor, which he uses under the codename "Groundhog."

Over a month later, the American criminal known as Egghead leads a team of super-powered mercenaries in an operation to blackmail Canada through the use of a nuclear warhead. As Wolverine, Logan leads a team of Flight trainees - Snowbird, Smart Alec, St. Elmo, Stitch, and Groundhog - against Egghead's forces; although Logan has periodically trained with the Flight over the past several months, this appears to be his first public appearance as a Canadian super-hero since his clashes with D'Von Kray. Although the mission is a success, St. Elmo perishes, Groundhog resigns, and other members prove themselves as yet unsuited for such missions.

Based upon this lack of preparation, Hudson will eventually divide the Flight into three divisions of increasing efficiency: Gamma, Beta, and Alpha, with Alpha Flight as the finalized public super-team.

At some point during these years, while stationed in Canada with the Flight, Logan has an affair with fellow member Narya, the half-goddess known as Snowbird (Uncanny X-Men #140). Unlike Logan, who is far older than he looks, Narya, although an adult in appearance, is chronologically and emotionally a child, far younger than she looks; the relationship ends badly.

Among the other Flight trainees with whom Logan periodically works is Gamma Flight's Wild Child (Marvel Comics Presents #51, Alpha Flight #118), a young man who was mutated by the Secret Empire using DNA from the superhuman mercenary Wyre, whom Logan had encountered at some point in the past. Logan, recognizing an inherent berserker nature similar to his own, advises against Wild Child's inclusion in the super-hero program, but Wild Child will remain until the program's cessation and, eventually, master his rages to join one of the various incarnations of Alpha Flight.

Logan himself recruits a future Alpha Flight member during these years: French-Canadian Jeanne-Marie Beaubier, later known as Aurora (Alpha Flight vol2 #9). One night Logan saw thugs accost Beaubier, who fought them off using her power of superhuman speed. Logan aided her in driving them off, introduced himself, and asked her to come with him to meet his friend, James Hudson.

Few other details of Logan's activities with Alpha Flight are known; he apparently spends most of these years abroad on various intelligence assignments, returning to Canada and Department H only on occasion.

Despite Department H's secrecy, Logan maintains some contacts outside the organization, including a young RCMP named Lightfoot (Codename: Genetix #1); at times Logan joins Lightfoot on hunting expeditions, although it is known that Logan refuses to kill for sport, preferring to track game in order to hone his skills only (Uncanny X-Men #109; Marvel Team-Up #117).

While tracking a terrorist assassin from Canada to Australia (Wolverine/Nick Fury: The Scorpio Connection), Logan meets David Nanjiwarra of ASIO, an Australian intelligence agency. When the two are stranded together in the Australian outback, Nanjiwarra helps Logan to survive long enough to reach civilization. Logan learns that Nanjiwarra, a descendant of native Australians, is disenchanted with ASIO work due to Australian prejudice, and Logan recommends that he seek work with SHIELD, which at this time is still in the process of organization.

At some point during these years, in Vladivostok, USSR (Marvel Fanfare #24), Logan again encounters Nick Fury; soon afterward, Fury is appointed to the directorship of SHIELD, and the two will not meet again for years. Logan himself apparently works directly with SHIELD on a few occasions during his Department H career; he is issued SHIELD identification for a time (Wolverine #50), although he is apparently never officially inducted into the organization, and, years later, he will have some familiarity with the layout of the SHIELD Orbital Platform (Uncanny X-Men #100) after it has fallen into the possession of the anti-mutant Project Armageddon.

Five years after his Iraqi mission (Wolverine #9), over three years after first assuming the costumed identity of Wolverine, Logan hunts down the mercenaries who helped take control of the US embassy and, over a period of days, kills all of them save for Malone, who commits suicide rather than give Logan the satisfaction of killing him. Malone had had psychologically and sexually abused a Canadian nun during her captivity. Her dying wish was that Malone should be made to suffer for what he had done.