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Golden Kamuy's manga and anime are broken into story arcs. The following are the arc names, a description of the arc's plot, and the chapters and episodes they comprise.
Saichi Sugimoto, veteran of the Russo-Japanese War, is on the hunt for gold to provide for the widow of his dead comrade. He learns of the tale of a stolen hoard of Ainu gold and the group of tattooed convicts who each hold a piece of the map to that treasure inked into their skin. To that end he joins forces with a young Ainu girl, Asirpa, who has a personal quest to discover the truth behind the Ainu gold.
Saichi Sugimoto and Asirpa encounter Yoshitake Shiraishi, the infamous Escape King and one of the tatooted convicts who have escaped from Abashiri Prison who provides a clue for another convict to the pair. During their investigations Sugimoto has a run-in with the 7th Division and Asirpa must rely on the aid of the Escape King to assist Sugimoto. Meanwhile Toshizou Hijikata, legendary vice-commander of the Shinsengumi, is recruiting fellow tattooed convicts to his side in pursuit of the gold.
Saichi Sugimoto and Asirpa travel to the coast following Shiraishi Yoshitake's lead that one of the 24 tattooed convicts - deranged serial killer Kazuo Henmi - is currently there posing as a fisherman. However, the 7th Division are also searching for Henmi. Sugimoto saves a fisherman whilst whaling but doesn't realise that his new friend is in fact the killer they are hunting. Meanwhile, Genjirou Tanigaki has nearly finished healing at the Ainu village only to recieve an unexpected visit from Ogata and Nikaidou who try to silence him so he won't report back to 7th Division about their desertion.
The small river port town of Barato once knew only one gang under the leadership of Tamotsu Hidoro. When Hidoro planned to give his gambling hall to his son, Shinpei, the Hidoro's right-hand man Umakichi Kusuda split the gang, waging war against the Hidoro clan for control of Barato. When the Hidoro's get their hands on a tattooed convict's skin it draws the attention of Toshizou Hijikata. To get closer to the skin, Hijikata offers his and Shinpachi Nagakura's services as bodyguards for the Hidoros to help them end the gang war and take out Umakichi's faction. Meanwhile, Hyakunosuke Ogata decides to work as a bodyguard for Umakichi, also hoping to get hold of the skin, by offering to finish the gang war except in Umakichi's favor instead.
On their travels, Saichi Sugimoto, Asirpa, Shiraishi Yoshitake and Kiroranke encounter a mysterious and untrustworthy fortune teller who encourages Yoshitake to gamble all his money on horse races. Kiroranke substitutes for a jockey and wins a race the yakuza tried to rig. Later, they agree to hunt a seemingly immortal "monster" bear for Eddie Dun in exchange for Asirpa's great-aunt's wedding garment. However, when the truth is revealed about the bear's supposed immortality the group winds up trapped under siege in the farmhouse with a coupleyakuza who've come to kill Kiroranke for not losing the race.
First Lieutenant Tsurumi meets and befriends eccentric taxidermist and grave robber Yasaku Edogai and convinces him to use his skills to make fake tattooed skins to confuse his enemies. However, shortly after Edogai finishes the skins both Sugimoto's Group and Hyakunosuke Ogata move in on his workshop and figure out Tsurumi's plan to make it harder for them to find the gold. Edogai and Sergeant Tsukishima flee into the local mines to escape with the skins with the other factions in pursuit.
A bandit couple known as O-gin the Viper and Keiichirou Sakamoto the Lightning Bandit target a small gambling den rumoured to have one of the tattooed convict skins. They team up with small-time thugs Kantarou and Kamezou to assist in the robbery. However, the skin is a fake and the den a set-up orchestrated by First Lieutenant Tsurumi and the 7th Division to catch the Lightning Bandit for the tattoos on his body since he is also one of the escaped 24 tattooed convicts. Meanwhile, Sugimoto's Group encounter venomous snakes in the forest.
When Sugimoto's Group meet up with Inkarmat and Cikapasi they explain that Genjirou Tanigaki has been accused of a crime he didn't commit by the local Ainu. His rifle was stolen by the academic Shiton Anehata, one of the 24 tattooed convicts, who roams the countryside violating and murdering animals. Because Tanigaki's rifle was used the local Ainu mistake him for the criminal and plan to punish him. The Ainu give Saichi Sugimoto and Asirpa three days to find Shiton and bring him to justice. Unfortunately, Shiton has already decided the next animal he wants to go after is a brown bear, jeopardising the legibility of his tattoos in the likely outcome the bear kills and eats him.
Trust is tested when, during a locust swarm, Inkarmat accuses Kiroranke of killing Asirpa's father and planning to betray the group. Furthermore, Ogata reveals Inkarmat's evidence must've been fed to her by First Lieutenant Tsurumi, implying she is a mole. Saichi Sugimoto concludes the only way to resolve who they can trust is still to speak to Nopper-Bou. The Ainu village has been attacked at nights by blind bandits who use the darkness and echolocation to their advantage. The bandits were convicts of Abashiri Prison blinded by working in a sulphur mine and led by one of the 24 tattooed convicts, Toni Anji. Toni and his men lay an ambush for the men of Sugimoto's Group while they're bathing at night at an inn, forcing them to fight in the forest without the use of their equipment or sight.
