Shadow Cry is a side story to the main plot of Persona 3 taking place during and making reference to the events of the main game. It is told primarily through Jin Shirato's point of view and details the daily life of the members of Strega.
The events of the story begin as Jin, Takaya Sakaki, and Chidori Yoshino after completing a revenge commission encounter a gathering of Cowardly Maya surrounding a young man. This young man is Izumi (イズミ), an original character created for the novel who, like Jin, is an artificial Persona user. Izumi had been presumed dead by the Kirijo Group after he had gone missing during an exploration of the Tartarus. Due to his low aptitude, his Persona appears as a formless mass he calls Nameless (名無し).
Izumi reveals that after escaping the Tartarus, he was saved by a young nurse who he lived with for a period of time. Unknowingly, he had contacted Strega to seek revenge for her death, though he cannot pinpoint the culprit, only knowing that it was a murder that was labeled officially as an accident. While Jin had initially turned down this request due to its feasibility, Takaya lets Izumi know Strega will take on this request.
While investigating the site of the incident, Jin discovers a milk bottle with a flower in it, but is attacked by a shadow-consuming monster. Shinjiro Aragaki saves him, but before he leaves Jin notes he is carrying the same type of flower. As the events of the story progress, it becomes apparent that the madness-consumed Izumi is this monster and Strega is forced to kill him.
- The original title of the novel contains a double-meaning as the kurai (クライ) of cry also makes reference to the kurai (喰らい) of to eat.