In a future transformed by the Smart Brain corporation, humanity faces the brink of extinction. Using experimental flowers that turn humans into genetic monsters called Orphnochs, Smart Brain has seized control of the world, with Orphnochs now comprising ninety percent of the population. The remaining humans, numbering only a few thousand, live in hiding, their last hope seemingly lost when Takumi Inui, the legendary Kamen Rider Faiz, was presumed killed in a battle with Smart Brain's forces. Since then, Takumi’s friend Mari Sonoda has led a resistance, launching desperate but futile attacks on the corporation’s headquarters to steal the top-secret Emperor Belts, which are said to be the ultimate Rider systems.

Unbeknownst to the resistance, Takumi survived, though with no memory of his past. He now lives quietly as a cobbler named Takeshi in a hidden human refuge ironically named Paradise, cared for by a young woman named Mina. Meanwhile, a trio of Orphnochs—Yuji Kiba, Naoya Kaido, and Yuka Osada—who dream of peaceful coexistence between humans and their own kind, attempt to broker peace. Their meeting is violently interrupted by Smart Brain's elite troops, the Riotroopers, led by their newest and most powerful weapon: the winged Kamen Rider Psyga. When Psyga attacks Paradise, the resistance fighter Masato Kusaka transforms into Kamen Rider Kaixa to fight back but is swiftly killed. During the chaos, a masquerade ball meant to boost human morale brings Mari face-to-face with Takeshi. The shock of seeing his old friend breaks through his amnesia, and Takumi Inui reclaims his identity and the Faiz Gear, transforming once more to destroy the attacking forces.

However, the resistance is wary of Takumi, as only Orphnochs are capable of safely using the Rider Gears, leading many to suspect he is one of the monsters they fight. Mina confirms this by revealing that her father found Takumi mortally wounded years ago, recognizing him as an Orphnoch, and implanted false memories to give him a peaceful life. She returns the Faiz Blaster to him before being shot and killed by a paranoid resistance member seeking the belt for himself. Yuji Kiba kills the traitor in self-defense and returns the belt to Takumi, but the resistance, fearing the three friendly Orphnochs, exiles them on a suicide mission: infiltrate Smart Brain and steal the Emperor Belts.

At Smart Brain headquarters, the mission goes horribly wrong. The monstrous Elasmotherium Orphnoch is unleashed, killing Yuka and devouring Naoya. Yuji is then tricked by a disguised Smart Lady into believing Mari betrayed them. He is captured, while Smart Lady uses his despair to force him to become the dark Kamen Rider Orga using one of the Emperor Belts. Back at Paradise, the human Keitaro Kikuchi uses an untested serum to temporarily become Kaixa, saving Mari from another attack, but the belt disintegrates. Mari is then kidnapped by Psyga and taken to the Smart Brain Super Arena to be publicly executed as a symbol of humanity’s defeat.

Takumi races to the arena, transforming into Faiz to save her. He battles the Elasmotherium Orphnoch and then duels Psyga in mid-air, ultimately destroying the celestial Rider with the Faiz Edge. However, Yuji Kiba appears, now transformed into the gold-armored Kamen Rider Orga, and attacks Faiz in a rage. Overpowered, Takumi is forced to reveal his ultimate secret: he is the Wolf Orphnoch. As the two clash in their true monster forms and then return to their Rider forms, the Elasmotherium Orphnoch breaks free and again threatens Mari. In a final act of redemption, Yuji regains his senses and sacrifices himself as Orga to save her, allowing Faiz to assume his Blaster Form and destroy the giant monster. With his dying breath, Yuji makes Takumi promise to achieve his dream of coexistence. As the stunned crowd watches, Takumi and Mari walk out of the arena together, leaving behind the ruined stadium to search for a place where humans and Orphnochs can finally live in peace.