"Persona Q: Shadow of the Labyrinth Side: P3" is a manga adaptation of the "Persona Q: Shadow of the Labyrinth" video game, focusing on the characters and events from "Persona 3." The story begins with the protagonists of "Persona 3" finding themselves transported to an alternate version of their school, Yasogami High, during a cultural festival. This mysterious setting is filled with labyrinths and populated by Shadows, malevolent creatures that the characters must combat using their Personas, manifestations of their inner selves.

The main characters include Makoto Yuki, the silent protagonist of "Persona 3," and his teammates from the Specialized Extracurricular Execution Squad (SEES): Yukari Takeba, Junpei Iori, Mitsuru Kirijo, Akihiko Sanada, Fuuka Yamagishi, Aigis, and others. They encounter the Investigation Team from "Persona 4," who have also been drawn into this strange world. Together, the two groups must navigate the labyrinths, uncover the truth behind their predicament, and find a way to return to their own realities.

The narrative explores the dynamics between the characters as they face challenges that test their resolve and relationships. Each labyrinth they encounter is themed around the fears and insecurities of the characters, forcing them to confront their inner struggles. The story delves into themes of identity, teamwork, and the human psyche, as the characters rely on their Personas to overcome both external threats and internal conflicts.

As the groups progress through the labyrinths, they uncover fragments of a larger mystery involving a mysterious girl named Rei and her companion Zen. Rei’s fragmented memories and enigmatic connection to the labyrinths become central to the plot, as the characters work to piece together her story and its implications for their own situation. The manga maintains a balance between action, character development, and the exploration of its psychological themes, staying true to the tone and style of the "Persona" series.