"Bungo Stray Dogs: Dead Apple" is a manga adaptation of the light novel and film of the same name, serving as a side story within the larger "Bungo Stray Dogs" universe. The narrative centers on a mysterious phenomenon in which ability users across Yokohama are found dead, their bodies surrounded by crystalline structures. The incidents are linked to a dangerous ability user named Tatsuhiko Shibusawa, whose power, "Dragon Head Portrait," allows him to manipulate the abilities of others, causing them to turn against their users. Shibusawa’s ultimate goal is to absorb the abilities of powerful individuals to transcend human limitations.

The Armed Detective Agency and the Port Mafia, typically at odds, are forced to collaborate to investigate the crisis. Atsushi Nakajima, a member of the Armed Detective Agency, becomes a key figure in the conflict due to his unique ability, "Beast Beneath the Moonlight," which Shibusawa seeks to control. Alongside Atsushi, Osamu Dazai, a cunning strategist with the ability to nullify other powers, and Ryunosuke Akutagawa, a ruthless Port Mafia operative, play pivotal roles in confronting Shibusawa. The story delves into the psychological struggles of its characters, particularly Atsushi and Akutagawa, as they grapple with their pasts and the nature of their abilities.

The plot unfolds as the characters navigate a surreal, fog-covered Yokohama, where Shibusawa’s influence creates a dangerous environment. The fog acts as a barrier, trapping ability users and forcing them to confront manifestations of their own powers. This leads to intense battles and moments of introspection, as characters must overcome their inner demons to survive. The narrative explores themes of identity, power, and the consequences of wielding extraordinary abilities, while maintaining a balance between action and character development.

"Bungo Stray Dogs: Dead Apple" expands on the lore of the series, providing deeper insights into the abilities and motivations of its central characters. It also introduces new dynamics between the Armed Detective Agency and the Port Mafia, highlighting their uneasy alliance in the face of a common threat. The story’s blend of supernatural elements, psychological depth, and high-stakes conflict makes it a compelling addition to the "Bungo Stray Dogs" franchise.