"Persona Q: Shadow of the Labyrinth Side: P4" is a manga adaptation of the "Persona Q: Shadow of the Labyrinth" video game, focusing on the characters and events from "Persona 4." The story begins with the Investigation Team from Yasoinaba—Yu Narukami, Yosuke Hanamura, Chie Satonaka, Yukiko Amagi, Kanji Tatsumi, Rise Kujikawa, and Naoto Shirogane—finding themselves transported to a mysterious, labyrinthine version of their school, Yasogami High. They encounter the protagonist and members of the Specialized Extracurricular Execution Squad (SEES) from "Persona 3," who are also trapped in the same strange environment.

The two groups quickly realize they are in the Velvet Room, a metaphysical space overseen by the enigmatic Igor and his assistants, Elizabeth and Theodore. They are informed that they must navigate a series of labyrinths to recover lost memories and escape. Each labyrinth is themed around the fears and insecurities of the characters, with Shadows—manifestations of repressed emotions—serving as the primary antagonists. The labyrinths are filled with puzzles, traps, and powerful enemies, requiring the teams to work together and utilize their Personas, manifestations of their inner selves, to survive.

As the story progresses, the Investigation Team and SEES uncover the truth behind their predicament. They learn that a mysterious girl named Rei and her companion, Zen, are central to the labyrinth's existence. Rei has lost her memories and is being pursued by a malevolent entity known as the Shadow Operative. The teams must protect Rei while unraveling the mysteries of the labyrinths and confronting their own inner struggles. The narrative explores themes of identity, memory, and the bonds of friendship, as the characters face their fears and grow stronger together.

The manga stays faithful to the game's plot, emphasizing the interactions between the "Persona 4" and "Persona 3" casts. Key moments include the fusion of the two teams' strengths, the resolution of Rei's backstory, and the final confrontation with the Shadow Operative. The story concludes with the characters regaining their memories and returning to their respective worlds, having forged lasting connections through their shared ordeal. The manga effectively captures the essence of the game's narrative, blending humor, drama, and action while staying true to the "Persona" series' signature tone and character dynamics.