On a post-apocalyptic Earth caused by global warming and the melting of the ice caps causing continents to sink, a high-tech Domed City was built as a refuge in Antarctica and was ruled over by the Admirals and their enforcers, the Guardians. It was an oppressive society where anyone seen as incompatible were reported and executed or sent to Prisoner Island. Long ago, citizens living in the Geothermal Conversion Device area, or “The Hole” that supplied power to the city led a revolt but it was quelled, and the 3rd Admiral opted to exile them on a passenger ship called the Ark rather than execute them. The Ark suffered from classism, particularly between the common people living in the Disposal Area and the rich, prideful people living in the Guest Cabin Area.

The Brown Rat Gang, a group of orphaned children consisting of members Tougo, Rikiya, Ren, Takuho, Dai, and Mei, lived on the Ark and thrived on stealing food and other items. Tougo's parents died from illness when he was young while Rikiya's mother was raised on the Ark and killed herself by jumping overboard, trying to bring the young Rikiya with her. They were friends with Kojirou, an alcoholic who wrote a story detailing the battles of the Kamen Riders against the Undead. Kojirou claims he could write the story because “God” came to him.

One day, the Rat Gang is found out by Ark crew after a failed theft attempt, and the ship captain and his subordinates head to the Disposal Area to punish them and take back their stolen items. Kenzaki is then found floating in the ocean and taken aboard the Ark. He’s able to give his name but doesn’t remember anything else. Citizens of the Guest Cabin Area object to taking Kenzaki aboard. The adults argue as the Rat Gang tends to Kenzaki’s wounds, when hordes of Undead suddenly arrive and swarm the ship. Tougo is shocked that Kojirou’s story seems to be coming true, and Kenzaki transforms into Blade to battle the monsters. He attempts to seal them away however his cards don’t work and just return to him instead. Blade proceeds to destroy all of the Undead and becomes shocked at seeing Earth’s three moons.

The Ark stops at an island, where the Rat Gang and Kenzaki disembark on passenger boats. Kojirou talks about how the world is divided into threes, in particular the Earth having three moons; and hearts, diamonds, and clubs being the three suits in a deck of cards. Kenzaki questions him about these. Kojirou remembers that in his story the spade was the fourth suit and there was only one moon, and comes to the realization that someone else made him write that story.

The group reaches a village on the island that’s mysteriously abandoned, and then find the villagers cowering in a cave. Learning that the Undead kidnapped all of the village’s children, the group heads to a volcano to find an Undead nest where a giant Mother Undead is sleeping and keeping several children tied up, seemingly to analyze them and then give birth to new Undead that can kill humans more efficiently. The Rat Gang destroys the Undead eggs and free the children, and attempt to kill the Mother Undead however it wakes up. Kenzaki as Blade Jack Form swoops in to battle the Mother Undead in midair. The passenger boats try to leave the island without Kenzaki, however the Ark begins leaving without them. The passenger boats get a call and learn that the Guest Cabin Area staged a mutiny and took over the Ark. They manage to get back onto the Ark and discover that the Guest Cabin leaders have already been slaughtered, and that it was imposter Undeads that actually took over the Ark. They make it to the steering wheel of the Ark just as Blade and the Mother Undead’s battle is taken to the ship. Blade changes into King Form and battles the Mother Undead and its minions as the Rat Gang and crew members retreat to safety. The Mother Undead is slain, and the crew moves to repair the ship before a storm rolls in.

The Ark struggles to keep afloat in the storm. Rikiya begins panicking when his room starts flooding with seawater, and when Tougo tries to save him he realizes that for some reason Rikiya and Tougo believed the other’s past was theirs. Tougo determines there really is a great power manipulating everyone. Rikiya and Tougo avoid drowning, however the Ark begins capsizing. Kenzaki changes into Blade and attempts to reattach the snapped-off anchor, but to no avail. Tougo touches Kenzaki and sees some of his past, where Kenzaki was taken in by a fishing boat that also sank; he can’t remember anything past that, just like Kenzaki himself.

The Rat Gang, Kenzaki, and civilians escape the sinking Ark on passenger boats as the sailors and captain stay behind, ultimately going down with it. The rough storm causes Dai and Mei to fall overboard, and Takuho dives in to save them. Kenzaki changes into Blade and dives in to rescue them, but is only successful in bringing back Dai and Mei and can’t find Takuho anywhere. The distraught Ren calls Takuho big brother, and Tougo remembers that the two of them actually were siblings in secret but seemed to have feelings beyond that that they couldn’t tell anyone. A laughing voice then rings out in Tougo and Kenzaki’s heads as the storm finally recedes. Three days after the sinking of the Ark, the Rat Gang’s boat still hasn’t found land. Ren lost her mind after losing Takuho, and would keep laughing like a little girl.

Meanwhile, Hajime had been living in the Domed City for 300 years and was working in a nursing home. Long ago, he left Amane when she was a teenager, fearing that eventually she would realize that he was immortal and was the monster that caused her so much sadness. When he returned to her decades later, she refused the idea of them living together again. Hajime then made a vow to live alongside people until the very end. An old man he was acquainted with passes away, and makes a last wish to have some of his ashes spread over the ocean. Hajime tries to sneak out of the city to spread the ashes when he encounters a woman Azumi being accosted by Guardians. Hajime helps her escape but winds up reported, and becomes a target of the Guardians. Azumi takes Hajime to the Hole to meet with an Anti-Admiral rebellion group.

Satsuki is a Domed City resident who grew up with Azumi in the Hole however he grew tired of life down there and snuck out, leading him to be arrested and taken in by the current Admiral as his servant, eventually becoming a captain of the Guardians. Satsuki is ordered by the Admiral to arrest Hajime; the Admiral is suffering from a malignant tumor and had less than a year left to live, and knows that Hajime’s lived in the city for 300 years and wants to know his secrets. Satsuki leads Guardians into the Hole to arrest Hajime, the latter noting that Satsuki has a similar appearance to Mutsuki and that Azumi resembles Nozomi. When they suddenly get attacked by Undead, Hajime turns into Chalice to destroy the monsters and is later knocked unconscious by Satsuki.

Hajime wakes up strapped to an operating table, where the Admiral plans to dissect him and learn his secret of immortality. Satsuki interrogates Azumi about her relation to Hajime. He returns to the Hole and is cornered by armed Anti-Admiral members, who demand Azumi’s release. More Guardians arrive and begin gunning down citizens, shocking Satsuki since he never ordered them to follow. Learning that the Admiral has ordered the eradication of the Anti-Admirals, Satsuki tries telling them to stand down but soon kills his subordinates. The Anti-Admirals launch their revolt against the Domed City, resulting in Hajime's dissection being halted. Azumi frees Hajime and they head to the Admiral's office to confront him, however Satsuki gets there first and is witness to the Admiral being slain by Undead.

Hajime and Satsuki agree to help Azumi overthrow the Domed City an