"Bungo Stray Dogs" is set in a world where individuals possess supernatural abilities tied to literary figures, with the narrative primarily centered around the Armed Detective Agency, an organization of gifted individuals who solve crimes and protect Yokohama. The story begins with Atsushi Nakajima, a young man expelled from an orphanage and left homeless. After encountering a mysterious man named Osamu Dazai, who is attempting to drown himself in a river, Atsushi becomes involved with the Armed Detective Agency. Dazai, along with his partner Doppo Kunikida, recruits Atsushi after discovering his ability to transform into a white tiger, a power linked to his namesake, the Japanese author Atsushi Nakajima.

The Armed Detective Agency operates as a counterbalance to the Port Mafia, a criminal organization that also employs individuals with supernatural abilities. The two groups frequently clash, with the Agency striving to maintain peace and justice while the Mafia pursues its own agenda. Key members of the Agency include Ranpo Edogawa, a brilliant detective with no supernatural ability but unmatched deductive skills, and Akiko Yosano, a doctor whose ability allows her to heal others at a great cost. On the opposing side, the Port Mafia is led by figures such as Ryunosuke Akutagawa, whose ability "Rashomon" creates a destructive shadow-like entity, and Chuuya Nakahara, whose gravity-manipulating power makes him a formidable adversary.

As the story progresses, Atsushi learns to control his ability and gains confidence in his role within the Agency. The narrative explores themes of identity, morality, and the struggle between good and evil, often blurring the lines between the two. Atsushi's past is gradually revealed, including his connection to the orphanage and the trauma that shaped him. The series also delves into the backstories of other characters, such as Dazai's enigmatic history and his former ties to the Port Mafia, as well as Kunikida's idealistic yet rigid sense of justice.

The plot intensifies with the introduction of the Guild, an American organization of ability users seeking to destabilize Yokohama. Led by Francis Scott Fitzgerald, the Guild's arrival forces the Armed Detective Agency and the Port Mafia into an uneasy alliance to protect the city. The conflict escalates with battles that test the limits of the characters' abilities and resolve. Later arcs introduce additional factions, such as the European-based organization Decay of the Angel, which further complicates the power dynamics in Yokohama.

Throughout the series, the interplay between the characters' abilities and their literary inspirations adds depth to the narrative. For example, Dazai's ability, "No Longer Human," nullifies other abilities upon contact, reflecting the existential themes of his namesake's work. Similarly, Akutagawa's "Rashomon" draws from the dark, introspective tone of Ryunosuke Akutagawa's literature. These connections enrich the storytelling, blending action with literary homage.

"Bungo Stray Dogs" balances episodic crime-solving with overarching plotlines, creating a cohesive narrative that explores the complexities of its characters and their world. The series combines supernatural action, mystery, and character-driven drama, making it a compelling entry in the anime genre.