"Persona 3 the Movie #3 Falling Down" continues the adaptation of the "Persona 3" video game, focusing on the protagonist Makoto Yuki and his companions as they confront the mysteries of the Dark Hour and the Shadows. The story delves deeper into the emotional and psychological struggles of the characters, particularly Makoto, who grapples with his role as the leader of the Specialized Extracurricular Execution Squad (SEES). The group continues their mission to defeat the Shadows and uncover the truth behind the enigmatic Tartarus tower, which appears during the Dark Hour.

The narrative intensifies as SEES faces increasingly powerful Shadows and internal conflicts. The group learns more about the origins of the Dark Hour and the connection between the Shadows and the human psyche. A key focus is the character of Ryoji Mochizuki, whose true identity as the harbinger of death, Nyx, becomes a central plot point. Ryoji's presence forces the group to confront the inevitability of death and the moral dilemmas surrounding their mission.

Makoto's relationships with his teammates, including Yukari Takeba, Junpei Iori, and Mitsuru Kirijo, are further explored, highlighting their growth and vulnerabilities. The film also introduces Aigis, a humanoid anti-Shadow weapon, whose bond with Makoto becomes pivotal to the story. Aigis struggles with her evolving emotions and her purpose, adding depth to the narrative.

The climax of the film revolves around SEES' decision to confront Nyx and the impending Fall, a catastrophic event foretold to bring about the end of the world. The group must weigh their desire to protect humanity against the potential futility of their efforts. The film ends on a somber note, setting the stage for the final installment in the series, as the characters prepare for their ultimate battle against Nyx and the forces of destruction.