Atsushi Nakajima vs. Ryūnosuke Akutagawa (Cargo Ship)

The second battle of Atsushi Nakajima vs. Ryunosuke Akutagawa is fought by Armed Detective Agency member Atsushi Nakajima and Port Mafia member Ryunosuke Akutagawa upon Atsushi's capture by the Mafia.

It happened at sea on one of the Mafia's cargo ships used for delivering arms and ammunition, where Atsushi is to be supposedly transported to the Mafia's bounty client.

Prologue
After Atsushi saves Kyōka Izumi and treats her throughout Yokohama, the Mafia interferes, and Akutagawa reveals having placed a tracker on Kyōka in order to trace Atsushi. The latter is then kidnapped after being wounded by Rashomon, while Akutagawa retrieves Kyōka back to the organization after accomplishing her "mission" as bait. Atsushi is taken to a truck and later brought to a cargo ship owned by the Mafia, which soon leaves at sea.

Later, Atsushi weakly regains consciousness and awakens to Kyōka opening the doors where he has been brought to. He is immediately grabbed outside by Akutagawa's ability and realizes they are at sea. Akutagawa furiously stomps on his earlier supposedly fatal wound and demands him to die to pave way for others, a curious animosity that Atsushi notices. Kyōka then points a gun at Akutagawa, though the latter quickly slices it with Rashōmon. He chokes and asks her to return to killing, claiming it as the sole thing that gives her worth to live.

After finding Atsushi's location courtesy of Ranpo Edogawa, Doppo Kunikida arrives on the Agency's speedboat and asks Atsushi to jump off the ship. Kyōka then holds Akutagawa in place and detonates a dynamite planted in the armory to sink the ship, as well as to allow Atsushi to escape. Akutagawa strangles Kyōka again, while Kunikida demands Atsushi to jump, persuading him that they cannot save Kyōka anymore. Atsushi rejects this notion and heads back to help Kyōka, which nonetheless earns Kunikida's support.

As Akutagawa prepares to finish Kyōka off, Atsushi swiftly saves her from him with his tiger speed. After placing the unconscious Kyōka at the side, Atsushi challenges Akutagawa to settle their strife once and for all.

Battle
A blast instantly signals the two to strike each other: Akutagawa launches Rashōmon, while Atsushi dodges it with his quick speed. Atsushi rips off a part of the deck and tosses it at Akutagawa, which Rashōmon slashes into pieces. However, the projectile is a diversion for Atsushi to leap at Akutagawa; he rams straight into the mafioso's face, only to be blocked by Rashōmon's Devoured Space. Atsushi is caught by various tendrils of Rashōmon and lifted up into the air.

Akutagawa claims that Atsushi is a mere weakling whose strength is but a delusion. Though he recognizes his own weakness, Atsushi points that he will defeat him, after which he frees himself from Rashōmon's grasp by unmorphing his tiger limbs to human arms. He instantly charges at Akutagawa and launches a stream of punches at Devoured Space until the invisible barrier fades. Atsushi then surmises that Devoured Space has an activation time limit for his defense. He throws another punch, but Akutagawa swiftly elevates himself in the air by using Rashōmon as a spire.

Akutagawa transforms his ability into beast-like heads that ragingly pursuit Atsushi. While running from the ability's appendages, Atsushi receives a blow from Rashōmon, plunging him into the deck's ruptured gas pipes that trigger and consume him in an explosion. Akutagawa deduces that the ship shall sink soon, presuming that he has beaten the weretiger. To his surprise, Atsushi uses an exploded debris to propel himself behind Akutagawa, afterwards punching the mafioso that smashes him back to the deck.

Akutagawa recounts his spartan training under Osamu Dazai's tutelage who easily overpowers him always. Fueling his rage and hatred, Akutagawa impales the deeply wounded Atsushi and expresses his apparent resentment towards the latter once more. Thinking of his slim chances of escaping, Atsushi is caught in Akutagawa's Higanzakura, but he manages to withstand the attack due to his regenerative ability, shocking Akutagawa.

Atsushi chides him for treating Kyōka as if she can do nothing else besides killing. Akutagawa rebuts that he merely granted her a value to her life especially given her powerful ability, but Atsushi shuns such thinking, believing that no one deserves to decide whether another person's life is worth anything.

With utter frustration, Atsushi rushes at Akutagawa, who instantly impales his torso with Rashōmon. The tiger's regeneration instantly activates, and Atsushi tears through Rashōmon, forcing Akutagawa to once more retreat into the air. He activates Sawarabi whose several spikes pierce through Atsushi from the ground. Resisting the attack, Atsushi leaps towards Akutagawa, but he inadvertently plays into the latter's hands as Akutagawa captures him in Rashōmon's giant maw, Prison Jaws.

As Atsushi falls off seemingly defeated, he uses the tiger's tail to coil around Akutagawa's waist. He quickly puts up his Devoured Space for Atsushi's incoming punch. His invisible barrier inevitably shatters, and Atsushi's punch lands straight on Akutagawa's face, plummeting his battered body into the sea.

Atsushi falls down to the deck with his strength drained, unable to stand any longer. A now conscious Kyōka lifts and supports him to escape the sinking ship. As an explosion knocks them off the deck, they fall off and land on the back of Kunikida's speedboat, who commends the unconscious Atsushi for a job well done.

Aftermath
As a result of the failed bounty operation, the Guild leader Francis Scott Key Fitzgerald calls off the affair with the Mafia, as well as his fellow co-conspirators, namely Dame Agatha Christie of the Order of the Clock Tower and Fyodor Dostoevsky of the Rats in the House of the Dead. Regardless, Fitzgerald remains confident that the Guild shall obtain their target – a certain Book – before anyone else can.

Meanwhile, Atsushi takes Kyōka to the office and worries that the Agency might not pardon her 35 murders. On the contrary, however, he finds the Agency members playing with Kyōka and even giving her treats, most particularly Ranpo.

After the battle, Ichiyō Higuchi locates and retrieves Akutagawa from the sea. He ends up with various external and internal injuries, as well as a comatose condition. Nonetheless, Ōgai Mori praises their efforts for doing their best in their bounty operation despite ultimately failing. However, with their primary attack dog in a dire situation, Mori questions Higuchi's place in the Mafia, which is also harbored by her fellow subordinates, including the Black Lizard.

Moreover, after Akutagawa massacred members of Karma Transit, the remnants of the organization take advantage of his vulnerable condition and target his life in retaliation.

Manga and Anime Differences
Atsushi throwing at Akutagawa a portion of the ship deck he ripped off turns out to be a diversion for Atsushi to sneak beside Akutagawa in the manga. In the anime, it does not appear to be a tactic to catch Akutagawa off-guard. Moreover, the manga depicts Atsushi attacking him in front, while the anime shows Atsushi attacking from behind Akutagawa.

The battle's aftermath, particularly on Akutagawa's side, is not shown in the anime, contrary to the manga where Higuchi is shown looking for and retrieving Akutagawa from the sea after his defeat.

Notably, the Guild, the Order of the Clock Tower, and the Rats in the House of the Dead are complicit in the Mafia's bounty operation. However, the anime portrays the Guild as the only party involved in the hunt for Atsushi. To cite another subtle difference, the supposed time for presumably delivering Atsushi to the Guild is shown to be 6:00 p.m. as shown on Fitzgerald's wristwatch in the manga, while his watch indicates it to be 4:00 p.m. in the anime.