Under unrevealed circumstances, Logan is recruited for Team X, a multi-national intelligence operation overseen by the Black Ops Special Services Section of the American CIA (Maverick #2). The Team X Project, also known as the Weapon X Program, although employing a number of super-agents for various missions, most notably in conflict with the super-agent programs of communist powers, is ultimately intended to selectively suppress those agents's memories and awareness of their super-powers, to be renewed as necessary, making them the perfect sleeper agents; memories are also implanted as deemed necessary (Wolverine #48-50), by the Team X Project's ally Psi-Borg (Wolverine #62), usually bonding such implants to actual memories of severe trauma.

Although Logan himself remains unaware of his mutant nature, the scientists of the Team X Project recognize his unique age suppression factor (Wolverine #50, 61) and, without his knowledge, isolate it and implant it within other agents; Psi-Borg is also promised such an age-suppression implant in return for his work but for unknown reasons does not receive it, a betrayal that will prompt him to seek vengeance on the members of Team X years later.

Another aspect of the Team X Project is the Shiva Scenario (Wolverine #50), a contingency in which heavily armored robots will be employed to terminate the agents as necessary; this scenario is evaluated by scientists Dr. Alexander Ryking, Dr. Kurt Marko, and Dr. Brian Xavier at the Almagordo Research Station, New Mexico (X-Men #12-13). The team's cover was to pose as atomic researchers.

In two years, Kurt Marko will double-crossed and murder his partner, Brian Xavier. The investigators will label the incident an accident, and Marko won't be charged with Xavier's death. Shortly after Xavier's death the Almagordo Research Facility will be shut down.

Sons of the first two men, Hazard and the Juggernaut, will later be numbered among Logan's enemies, while the son of the third, Professor X, will prove to be one of his closest friends and advisors.

Unaware of the full nature of Team X's work, and perhaps preferring to work with others after his recent experiences, Logan joins the Team X Project.

Among the other members of Team X (Wolverine #48), Logan is surprised to find Sabretooth and shocked to find Silver Fox, whom he had thought long dead. Silver Fox herself, either as a result of trauma or other factors, remembers little of her assault by Sabretooth at this point. At her instigation Logan, his own memories of the event clouded by the same trauma that the Team X Project will use as the basis for his memory implants, sets aside his enmity for Sabretooth. It is in fact possible that the memories of all three are suppressed by the Team X Project.

Logan's other Team X colleagues include John Wraith, a.k.a. Kestrel, and Mastodon. Logan's closest friend on the team is Sgt. David North, also known as Maverick (X-Men #6), a former West German freedom fighter. Other Team X operatives are known by the code-names Vole and Wildcat (Wolverine #50); according to one account, the mutant shapechanger Mystique, under the name of Leni Zauber, also assists Team X on occasion (Team X/Team 7).

Team X's Canadian facility is located in Alberta, Canada, adjacent to a Blackfoot burial ground (Wolverine #52). In the course of his near-decade of service, Logan eventually reaches the rank of major in the United States Armed Forces (Wolverine #50) under the command of Team X's army liaison, Major Arthur Barrington (Maverick #2). Perhaps in honor of his past on the frontier, so vividly recalled by Silver Fox, Logan adopts the codename "Wolverine" for what appears to be the first time (aside from his questionable activities during 1936).

As a member of Team X, Logan is often partnered with Sabretooth. In 1963, Logan, Mastodon and Sabretooth are operational in Cuba when Silver Fox betrays them to Cuban soldiers (Wolverine #49, 61). Fox's treason may be due to a deviation in her memories of the attack by Sabretooth, leading her to recall the full extent of the attack and to erroneously believe that Logan abandoned her. This may be an extreme reaction to the Team X memory implants, perhaps due to an interaction with the unknown procedure which arrested her aging. President Kennedy and Lee Harvey Oswald were shot while they were there, this somehow affected their mission. (Wolverine #49-50)

Following this betrayal, Silver Fox becomes a terrorist (Wolverine #49-50), clashing with her former teammates on a number of occasions, and eventually rises high within the ranks of HYDRA. The Team X Project loses track of her at some point in the 1970s.

Early A.D. 1960s: Victor Creed was assigned to East Berlin to assassinate a scientist who possessed information that worried his superiors and to bring back a fellow spy. Creed arrived to find that the spy, Leni Zauber (Mystique), had killed the scientist herself (with poison, to which she claims spending a year building up immunity). The two were chased through the city by Kommandos. They fled from East Germany, crashing through the Berlin Wall at Checkpoint Charlie.

Creed and Zauber then began an affair, and Creed did not report to his fellow agents for a month and it was feared that he had gone rogue.

In actuality Leni Zauber was Raven Darkholme, who had taken the form of Zauber as a convenient method to disappear when such means were called for. Such a situation arose when Darkholme discovered plots against her life. The mutant arranged for the death of the real Zauber. Darkholme had never told Creed that she was not the true Leni Zauber, and did not inform him that she was still alive. Creed, believing that his lover was dead, returned to his unit and teammates Logan, Wraith, and Maverick. (Sabretooth #3-4)

Nine months later Darkholme gave birth in America to a son, Graydon Creed. 'Leni Zauber' holds the infant Graydon Creed, frustrated by his constant crying. The shape-shifter had no interest in raising a child and treated him coldly, rarely seeing or visiting him as he grew up. She planned to give him up for adoption, but contradicts her later story that she abandoned him during his late childhood (X-Men Forever 2, Sabretooth #3, X-Men Unlimited 4).

Much later, Sabretooth's telepath Birdy delves into Graydon Creed's memories, and finds one of him as a child, spying on his mother and discovering that she is a mutant shapeshifter. Mystique is not impressed, with either the act or the boy in general, and disdainfully scolds him (Sabretooth #4).

Victor Creed, a CIA agent, and Amichai Benvenisti, an agent of the Mossad (Mystique in disguise), are meeting Destiny at a rendezvous in Jerusalem. Amichai is horrified to see her strung up from the rafters, but as he goes to free her, they activate a booby trap. Sabretooth later awakens to find himself chained up by a HYDRA goon named Catalyst.

Destiny wakes up Mystique inside their cell, and Raven is overjoyed to see her safe. Destiny tells her that Catalyst is extremely dangerous, connected to both the Israeli mafia and HYDRA. He shows up, returning Sabretooth to the cell, and is surprised to find a shapeshifter rather than Amichai, but is nonetheless pleased. He beats up Mystique when she tries to defend Destiny, and uses his mutant power to alter her chemical reactions, telling her how he'll torture her. Destiny tries to get him to leave Mystique alone, offering to go with him and telling him "mine will be the last face you see before your death!" Mystique then uses the opportunity to break herself and Sabretooth out of the cell.

Sabretooth bursts into Catalyst's torture cell as he interrogates Destiny. She seizes the opportunity of the distraction by kicking her tormentor into a tub of water, which electrocutes him. Though the others are sorry he didn't suffer more, Amichai worriedly frees and comforts Destiny, who predicts bad things for the future. (Sabretooth and Mystique #1-3)

Interpol agent Sean Cassidy and his superior Daniel Peyer infiltrated the offices of Almandovar, a mobster who had been targeted for death by a number of warring crime syndicates. While in the process of looking for the mobster Cassidy was discovered. Almandover was about to kill Cassidy when he was interrupted by Deadpool, a mercenary who had been hired to capture the mobster. When Almandover turned his weapon on Deadpool, the mercenary shot him dead. Deadpool quickly left the scene, but not before telling Cassidy that he would find out who he was and that Cassidy was now in his debt. (Deadpool v2 #2)

In keeping with US interests of the times, Team X is often dispatched to Cuba and southeast Asia (Wolverine #61), although details of these missions are sparse; in later years, Logan will prove capable of recognizing the jungles of Vietnam at a glance (Uncanny X-Men #226). According to one account, the group also ventures into the Sultanate of Numidia in the Middle East (Team X/Team 7), where they encounter a similar team of super-agents sponsored by another government agency.

In 1968, Logan, with Sabretooth as backup, returns to the USSR when he is dispatched to Tyuratam to sabotage a moon voyage by assassinating the Soviet super-agent Epsilon Red (Wolverine #65-68); the mission is called off before Logan can do so, but Sabretooth murders Epsilon Red's wife on a whim. It is also during this period that Logan, Sabretooth, and Maverick are sent on a joint NATO operation (X-Men Unlimited #15, Maverick #2) to recover a foreign national in East Germany.

In Logan's final known mission with Team X, he, Sabretooth, Maverick, and John Wraith are again dispatched to East Germany to sabotage a Soviet super-soldier program in Berlin and retrieve an experimental piece of technology known as the carbonadium synthesizer, along with a double agent named Janice Hollenbeck. Carbonadium is the best form of adamantium.

Team X is confronted by another super-agent, Arkandy Rossovich - Omega Red (X-Men #5-7, Wolverine #60). Omega Red, whose power was to produce lethal pheromones and weilded carbonadium tentacles as strong as Wolverine's claws, will later become one of Logan's deadliest enemies.

As they conducted surveillance on the building where both were located they discovered Omega Red undergoing the process of being bonded with carbonadium. Creed ordered Logan to retrieve the C-synthesizer and for Maverick to locate Hollenbeck, while he destroyed the super-soldier experiment. All three completed their assignments, and even though Creed interrupted Omega Red's bonding to carbonadium he didn't succeed in killing the Russian.

The three agents and Hollenbeck were discovered by the Russians and forced to retreat to the tenth floor of the building. The four were about to jump from a window when Rossovich attacked them. Creed began to panic, and considering Hollenbeck a liability to their escape, used his gun to kill her in cold blood. Creed then threw thermite grenades at Omega Red. The three agents, with Logan carrying Hollenbeck's body, then jumped from the tenth story window. The grenades exploded behind them, killing Rossovich. Logan and Creed's mutant healing factor, and Maverick's body armor and his mutant ability to re-channel kinetic energy, allowed them to survive the fall. The three agents then fled for the river.

Logan told Creed and Maverick that he must have lost the C-synthesizer in the fall. However he still possessed it, and hid it within Hollenbeck's body. The trio were retrieved shortly afterwards from the river by fellow operatives. Twenty-four hours later the team were being debriefed when Logan attacked Creed for killing Hollenbeck. Security guards separated the two, but Creed threatened Logan that one day he would have revenge.

Logan's rapid recovery from the fiasco leads him to finally realize that he is a mutant with enhanced healing abilities and other superhuman powers (X-Men #6).

Disturbed by this revelation and unwilling to continue working with the murderous Sabretooth, Logan resigns from Team X (X-Men #6). Team X itself disbands shortly thereafter (Maverick #2), perhaps due to repercussions from Sabretooth's actions or Logan's resignation. Logan's Team X files are officially rendered dormant on October 5, 1972 (Wolverine #50). Of Logan's Team X years, he will claim only that he was a "commando" prior to entering Canadian Intelligence (Uncanny X-Men #163).

Shortly afterwards, The C.I.A. Security Committee, believing that sleeper super-soldiers in the general population may potentially pose a threat, initiated the Shiva program. The program would use robots as tools, send them against opponents, and analyze their weaknesses. Through this the program would be able to create androids that would be immune to their predecessor's cause of defeat. Shiva was also armed with the means to activate the sleeper super-soldiers' brain implants. When the memory alterations had been performed, the candidates were turned over to different research and development teams, which then experimented on and gave to the candidates new abilities or hidden weapons. After receiving her cybernetic implants one of the candidates, Silver Fox, was placed back in the general population. However Silver Fox quickly disappeared, and the C.I.A. lost track of her. Silver Fox joined HYDRA, and over the next few years slowly rose up through the subversive organization's ranks. (Wolverine #50)

Having resigned from Team X but unsure of how to deal with the knowledge that he is a mutant, Logan goes to work for an unnamed branch of the Canadian Defense Ministry (Logan: Secret Society), an agency "so secret that not even the Prime Minister knows of its existence" and for which he will work for years.

Operating out of Ottawa (Wolverine #66), he is partnered with Neil Langram, who, like Logan, is a mutant, although the nature of his superhuman power has never been revealed. As a part of this agency, Logan, eventually reaching the rank of commander, is equipped with false I.D. cards (Wolverine #66) from a wide variety of intelligence agencies, including the Federal Air Marshalls, the KGB, the CIA, the GRU, MI-5, Shin Beth, and the UN Peace-Keeping Force; it may also be during this period that Logan acquires a (presumably) false I.D. as "Jim Logan, Detective" with the Nassau, NY, Police Department, an I.D. which he maintains in recent times.

Emerging from Team X's ultra-covert activities, Logan renews his partnership with Cracklin' Rosa (Classic X-Men #26) on at least one occasion, during which he nearly crosses paths with Interpol agent Sean Cassidy, whom he will meet again in later years. Among Logan's civilian friends during this period is a young woman named Rose, who may be Cracklin' Rosa's daughter. When operational in Canada, Logan drives a Lotus-Seven (Wolverine #48) and, despite a personal dislike of guns (Wolverine #-1), carries a Colt 1911A1 (Wolverine #76), although he often prefers to wield a pair of blades as personal weapons, as he did during his freelance days. As he did while a member of Team X, Logan uses the codename "Wolverine."

One account indicates that it is also during his first few years with this agency that Logan takes up the role of Montra Warrior of the Kage Ryu' for the third time; once again, he proves victorious (Wolverine/Shi: Dark Night of Judgment).

At times, Logan uses the alias "Agent Ten" (Untold Tales of Spider-Man #-1). As Agent Ten, Logan works in cooperation with a US organization known only as "the Agency," overseen by his old friend Nick Fury.

On at least one occasion, Logan also works with Richard and Mary Parker, married government agents who, months after their first meeting with Logan, have a son, Peter, who will eventually become the noted super-hero Spider-Man, whom Logan will encounter on many occasions. It will be over sixteen years before Fury goes on to head the international espionage agency known as SHIELD.

At one point, Logan is given a special assignment to investigate corruption on the Canadian docks. In the course of this undercover investigation, he encounters the sorcerer Abdul Alhazred (Marvel Comics Presents #154), who is involved in the illegal activities. Logan proves no match for Alhazred's magic, and the experience leaves him deeply shaken. Years later, the mere sight of the mark of Abdul Alhazred will prove so inherently frightening to even Logan's bestial persona that the shock of it will snap him back to humanity when temporarily out of control (Marvel Comics Presents #63).

On another mission, Logan travels to the USSR to accompany the defecting scientist Dimitri Suhkarov and his young daughter Viktoria from Soviet territory (Wolverine '97 Annual). Doctor Suhkarov is murdered by the Russian agent Volk, but Logan is successful in bringing Viktoria Suhkarov to Canada; Logan will be a close friend to Suhkarov as she grows up, and she herself will eventually work for the Canadian Secret Service.

At some point during his years of service, Logan's superiors in the unnamed agency offer him the opportunity to become a cyborg (Uncanny X-Men #132), his already heightened skills and senses to be augmented further by cybernetic implants. Logan is intrigued by the notion but ultimately decides against it.