"Kindaichi Shōnen no Jikenbo: Operaza Kan Saigo no Satsujin" is a mystery anime centered around Hajime Kindaichi, a high school student with a knack for solving complex crimes. The story unfolds during a school trip to an opera house on a remote island, where Kindaichi and his classmates are invited to perform in a play. The opera house, steeped in eerie history, becomes the setting for a series of gruesome murders that mirror the tragic events of a past performance decades earlier.

As the play rehearsals progress, a masked figure begins targeting the cast and crew, leaving behind cryptic clues tied to the opera's dark legacy. Kindaichi, with his sharp deductive skills and attention to detail, takes on the challenge of unraveling the mystery. He is aided by his childhood friend, Miyuki Nanase, who provides emotional support and occasionally assists in piecing together the puzzle. The narrative delves into themes of revenge, betrayal, and the lingering impact of past tragedies, as Kindaichi uncovers the connections between the present murders and the opera house's history.

The plot is driven by a series of intricate puzzles and red herrings, keeping viewers engaged as Kindaichi methodically works through the evidence. The characters, including the suspects and victims, are developed with distinct personalities and motivations, adding depth to the unfolding mystery. The story builds to a climactic reveal, where Kindaichi exposes the killer's identity and the reasons behind the murders, tying together the threads of the past and present in a satisfying resolution. The anime maintains a tense atmosphere throughout, blending elements of classic detective fiction with the theatrical backdrop of the opera house.