The story unfolds in a world where humanity faces extinction from the Unknown, supernatural beings that exclusively target individuals possessing latent psychic abilities. The crisis escalates when a top-secret military facility, the GA Psychic Educational Institute, is attacked by the Unknown. In the chaos, two young psychics, a boy named Rei and a teenage girl named Sayaka who possesses the ability to foresee the future, manage to escape.

Months later, Sayaka is discovered by a young amnesiac named Shouichi Tsugami, who secretly transforms into the powerful being known as Kamen Rider Agito. She reveals the horrors of the research facility and her fear of being hunted again. Shouichi, along with Makoto Hikawa, a police officer who dons the powered armored suit G3-X, and the feral Ryo Ashihara, who transforms into the monster-like Kamen Rider Gills, become her protectors. They must fight the relentless Unknown, but a new and more terrifying threat soon emerges from within the military itself.

A rogue faction within the military, led by the ambitious Risa Fukami, has stolen the blueprints for the G3-X system from its creator, Sumiko Ozawa. Their goal is to complete Project G4, a new prototype armor designed to be the ultimate anti-Unknown weapon. Unlike its predecessors, the G4 system possesses immense power, comparable to Agito’s own strongest forms, but it is flawed and highly dangerous, as the energy feedback fatally strains the nervous system of its wearer. To overcome this fatal flaw, Fukami seeks to harness Sayaka’s precognitive abilities. By linking the G4 armor to a psychic who can predict enemy movements, the system can react instantly, theoretically achieving perfection. The pilot chosen for this suicide mission is Shiro Mizuki, a broken and prideful soldier who lost his will to live and sees the G4 armor as a chance for a glorious death.

The narrative builds towards a final confrontation where the heroes must separate their battle against the Unknown from their fight against human militarism. While Agito and Gills clash with the powerful Unknown Lords, Hikawa, in the G3-X suit, faces his ultimate test against the far superior G4. The fight is not merely physical but a clash of ideals about the nature of heroism and sacrifice. As the G4 system begins to malfunction under its own power, a determined Mizuki refuses to surrender, pushing his body past its breaking point. The film culminates in a decisive battle where the heroes must stop the G4 from causing further destruction and secure a future for the psychics who are being hunted by both monsters and the military.