On September 1, 1939, Germany invaded Poland, sparking World War II. Logan, as a westerner, is no longer welcome in Japan. He returns to Madripoor, where he uses his newer skills, including swordsmanship, to aid Seraph against the Hand; Logan's enmity toward the Hand will eventually come to the notice of Stick (Wolverine #100), leader of the Chaste, a sect of warriors who have opposed the Hand for untold years.

In 1940, Dr. Myron MacLain began work for the American government, experimenting to create a super-metal for which to build tanks. Months later, an experiment of his to fuse Wakandan Vibranium with iron alloy was successfully completed when an unknown x-factor entered the mixture while MacLain was asleep. Awaking, MacLain poured the blend into a tank cover mold, and after hardening, MacLain discovered that the metal was almost completely impervious. MacLain studied the disk for months but was unable to discover how the two metals had combined to form this new one, which MacLain named adamantium. MacLain would spend decades experimenting, attempting to duplicate his original success.

By June 1941, the adamantium disk created by Dr. MacLain was presented to Captain America by American president Franklin Delano Roosevelt for use as his new bulletproof shield. The disk was aerodynamic, and Captain America began using it as an offensive as well as defensive weapon (Captain America v1 #255).

Meanwhile, the Hand, a Japanese ninja assassin squad, began making infiltrations onto the island nation of Madripoor (Uncanny X-Men #268).

By late summer 1941, Baron Wolfgang Von Strucker kidnapped Natalia Romanova from Soviet soldier Ivan Petrovitch (who had found Natalia in 1940 and decided to raise and care for Romanova as she grew up). Captain America was assigned to Madripoor to meet up with Petrovitch and to track the whereabouts of Baron Strucker. While rescuing Petrovitch from a Hand attack, Captain America was himself rescued by Logan, who was trying to prevent Hand infiltration of Madripoor. The three teamed up to rescue Romanova from the Nazis and the Hand. With Logan's help, Captain America and Major Petrovitch escaped Madripoor, and Petrovitch and Romanova made their way back to the Soviet Union (Uncanny X-Men #268); during the war, Strucker will work with Japanese criminals in the foundation of HYDRA, a worldwide terrorist organization.

As far as is known, Logan and Captain America do not meet again for decades, when Logan has joined the X-Men and Captain America, his youth preserved by suspended animation, has joined the Avengers; to this day, it remains unclear whether or not Captain America is aware that the X-Man Wolverine is his wartime comrade Logan.

In the fall of 1941, Nicholas "Nick" Fury enlisted in the United States Army. He was assigned to Pearl Harbor, Hawaii (which gets bombed December 7, 1941), and quickly rose to the rank of sergeant. During the War Fury also became a heavyweight boxer.

Eventually, perhaps at the urging of Seraph to embrace responsibilities in his homeland, Logan returns to Canada and again enlists in the Armed Forces. Achieving the rank of corporal, he is sent to Greece where, under the alias "Canada," he teaches resistance fighters the use of explosives and the Fairbourne dagger, which he himself wields on a number of missions.

By June 6, 1944, Corporal Logan is a member of the First Canadian Parachute Batallion at Ranville (Wolverine #106), Normandy (Wolverine #34, 85), where he and other Canadian soldiers parchute behind enemy lines from a burning C-47. Using only his knife, Logan managed to fight off their German attackers. Canada's role in the Normandy invasion is featured in the 6/7/44 edition of the Toronto Star (Wolverine #79), a copy of which Logan retains as a souvenir to this day.

Among the Nazi soldiers that Logan encounters on this mission is Bloodscream (Wolverine #78). Ages ago, Bloodscream was turned into an unnaturally strong, shape-shifting vampire by the pagan necromancer Dagoo, doomed to suck the life out of his victims until he finds the "blood of a man who ageth not." He sought to find that man in Logan, whom he first encountered in 1944 at the Battle of Normandy.

Also, Logan was in Greece helping out some people fight the Nazis. Those people would later be hired to tend the gardens in Elektras family's mansion. (Wolverine #106) On his visit with Elektra years later to visit her family in Greece, Stavros, one of her friends there, said that he knew of a Canadian from World War II. During this time, this Canadian had given him a dagger to use offensively. When asked by Logan if he remembered the name, he just replied "We called him 'Canada'". Near the end of the novel, we see Stavros with the dagger...and on it was enscribed the words "Cpl. Logan".

It may also be during this period that Logan first meets Nick Fury (Marvel Fanfare #24, Uncanny X-Men #252), a noted American soldier who will, like Logan, go on to become famous in the espionage field. Fury's eye injury prompted Logan to call him by the same nickname Logan once used, "Patch."

According to one account, Logan and Fury, not yet injured, are already acquainted when both are part of a joint American-Canadian intelligence operation (WildCATs/X-Men: The Golden Age.). On this occasion, Logan is dispatched by Canadian Intelligence to retrieve an arcane scroll from Nazi Germany. During this mission, he again encounters Eikert, now a Nazi officer, and is briefly drawn into a minor skirmish between two warring races of extraterrestrials. In this account, Logan claims to "have a history" with a being named Kenyan, who is intimately involved in this war.

Few other details about Logan's World War II service are known. He is known to have spent at least one winter below Monte Cassino (Uncanny X-Men Annual #4), in Italy, presumably serving with Allied forces. Decades later, under the influence of a powerful hallucinogen, Logan will, in a dream, live through the Nazi invasion of an unspecified country, as well as a brief encounter with Adolf Hitler and the cyborg Nazi Geist. (Wolverine #21); it is not known if the events of this dream are based in reality. Logan will also later speak of the British invasion of Dresden (Wolverine #61) as though he had witnessed the aftermath of that battle, but, again, whether or not this is the case is unknown.

August 14, 1945. The Japanese surrendered, ending the Second World War.

Logan resigns from the military and again travels to Japan, hoping to participate in the reconstruction of that nation following the collapse of the imperial government. During this time, in Kyoto, Logan encounters a man named Kimora (Logan: Path of the Warlord), who, unknown to Logan, is an extradimensional despot temporarily stranded on Earth; the two men battle. Logan is victorious, but does not kill Kimora when given the chance. The precise circumstances under which the two came into conflict are unknown, but years later Kimora will note that he "once saw in [Logan] a worthy adversary."

Logan may also meet the young Asano Kimura (Wolverine Limited Series #1, 3) during this time. Years later, Kimura will join the Japanese Secret Service and again encounter Logan, who will eventually categorize him as one of his oldest and best friends. Although the similarity of the names "Kimora" and "Kimura" is suggestive, no known connection between the two men exists.

From Japan, Logan travels to China, where the People's Republic is forming (Uncanny X-Men #363); he may also spend some time in Europe. Logan is deeply troubled by what he sees during the rise of communism in both "Stalin's Russia" and "Mao's China" (Daredevil #249), as some of the most talented citizens of these nations are imprisoned or slain for their refusal to submit to totalitarian rule.

He and Black Crane meet again during this period, and Logan incurs a "blood debt" to Crane which remains unpaid to this day (Deadpool #27); it may be during this period that Logan was temporarily enslaved by unknown parties (Uncanny X-Men #238), and his freedom may be the "blood debt" he owes to Black Crane. Logan keeps this period of enslavement, like many other aspects of the first half of his life, under great secrecy.