This movie is an alternate ending to the series, taking place after the events of episode 46. With only six Riders remaining in the Rider War, Shirō Kanzaki feels that time is running short.
Mothra and her fairies return to Japan to warn mankind that they must return Kiryu to the sea, for the dead must not be disturbed. However Godzilla has survived to menace Japan leaving Kiryu as the nation's only defense.
JSDF pilot Akane has a fateful encounter when a new Godzilla emerges in Tateyama. As a countermeasure, a cyborg named Kiryu is constructed from the remains of the original. The machine is discovered to harbor the restless soul of the original monster as Akane must learn to find value in her own life as well.
Shouichi encounters a teenage girl called Sayaka, who ran away from a military facility because of an attack by the Ant Lords. Sayaka has a supernatural ability to foresee the future. Risa Fukami, of the military group GA, wants to use that power to enhance the newly-made G4 System, which was based upon designs stolen from Ozawa. Now, Agito and Gills must fight to stop the Ant Lords' attack, as G3 and G4 settle their score.
Shouichi encounters his old friend and caretaker Dr. Higashi Kunieda. Dr. Kunieda, a friend of Yoshihiko Misugi, took care of him while he was hospitalized with amnesia. After catching up on a year of separation Shouichi abruptly leaves to house to fight an Unknown as Agito Burning Form. Unfortunately, after the Unknown flees Shouichi loses control of himself and attacks Dr. Kunieda, who followed Shoucihi and watched him transform. Dr. Kunieda managed to calm him down but Shouichi becomes to afraid of himself and runs away.
Takeshi Hongo is a promising young man with a passion for motorcycle racing. However, his dreams are suddenly ruined when he gets kidnapped by Shocker, the evil secret organization planning to dominate the world. After being remodeled into a cyborg, Takeshi escapes and swears to protect the world from the inhuman monsters.
A man named Shoichi Tsugami has lost his memories. He doesn’t know who he is, where he came from, or how he came upon his peculiar circumstances. Tsugami, seemingly for no reason, transforms into a powerful superhuman, Agito, whenever in the presence of the beings referred by the police as the “Unknown”, a race of powerful monsters that have been causing murders around Tokyo, targeting certain people as their prey. In response, the police department unleash their newest weapon: the G3 powersuit. G3 and Agito don’t know whether they should join up and defeat the Unknowns, their common enemy, or to combat each other, keeping the mysteries that entwine them separate. Ultimately, even more mysteries unfold, with the appearance of Kamen Rider Gills, who is on a search to uncover why his father committed suicide. These mysteries and others collide, as the true nature of Agito would ultimately determine the fate of humanity.