Fifteen years have passed since Shinichi Ichikawa, formerly known as Zebraman, defeated the alien menace that threatened Earth. In this dystopian future, Tokyo has been renamed Zebra City, and its citizens experience the oppressive rule of the authoritarian Zebra Queen. Zebra City enforces Zebra Time twice a day, giving residents free rein to commit crimes for five minutes with no legal repercussions. During a particularly violent episode of Zebra Time, Shinichi suffers amnesia and finds himself in the care of a group that opposes Zebra Queen's regime. They inform him of his legendary status as Zebraman, a persona he no longer remembers. Despite his amnesia, latent powers within Shinichi hint that he may hold the key to liberating the city.

Amid the chaos, Shinichi begins to uncover the dark truth about Zebra Queen's rise to power and her connection to his former nemesis. As he struggles to piece together his fragmented memories, he encounters character Yui, who inadvertently becomes embroiled in the conflict. With the Zebra Police tightening their grip and the Queen's sinister plans unfolding, Shinichi must reawaken his Zebraman alter ego. Time is running out, and the stakes are higher than ever. His journey from powerless amnesia patient to fledgling hero sets the stage for a climactic battle that could determine the fate of Zebra City and its oppressed citizens.