Kuniko and Momoko bump into Kunihito, who masquerades himself as an otaku. He threatens them to stay away from the area but both of them decide to follow him anyway. Using a virtual simulator supplied by the old otaku shopowners, Kuniko hacks the security camera in the shop to see what Kunihito is up to. Kunihito and Leon, one of Ryoko's men, question a shopowner on who may have recently purchased a specific nanochip. After using a piece of mimic armor to bribe the owner, he reveals that an American finance company called Serpent purchased one. Kuniko discovers Karin's presence. Miiko tells stories of the livelihood of Duomo residents to Mikuni and the girl longs to go outside. Kuniko and Kunihito are forced on a date by Momoko. The pair question and criticize each of their faction's motives. A bomb shower occurs and the two seek shelter. Kuniko and Kunihito formally introduce themselves and learn more about each other's lifestyles, however their conversation goes sour and Kuniko attacks Kunihito in anger and escapes, losing her boomerang in the process. Kuniko brings back the mimic armor sample to show her grandmother and Takehiko. Karin speaks to a governmental minister, asking him if he wants to take down Serpent.

A heated discussion erupts among Metal Age members on whether Kuniko will take over Nagiko's place as leader. A flashback shows Kuniko's childhood and her first meeting with Momoko and Miiko. After beating Momoko up, Sayoko demands to know how he got the earring. When Momoko refuses to talk, Sayoko resorts to using truth serum to make him tell the truth, but he has a tolerance to the medicine and reveals nothing. By watching Sayoko, Momoko deduces that she was once a mother, this causes Sayoko to strangle him. Mikuni tricks Miiko to a game of hide-and-seek but quietly sneaks outside the palace. She passes out from pain when sunlight envelops outside. At this time, Hiruko prophesies over the sun, moon and land, stating the time has come to listen to Amatsumihashira, the pillar of heaven. Klaris returns control of Medusa over to Karin. Mikuni reveals to Sayoko that she heard a voice, which shocks Sayoko. Ryoko makes a press conference announcing her new position as prime minister, which angers Kuniko and Metal Age. After being told to standby, Sayoko resorts to take Mikuni to where the sun shines. Kuniko makes her decision to become leader of Metal Age. She accepts the sun blade from Nagiko and causes a resonance with the other blades. Ryoko sends stealth carriers to attack the facility where Medusa is kept.

Ryoko decides to make Miiko the next vessel for Lord Hiruko. Kuniko returns with Momoko back to Duomo to think of their next step. After being welcomed back by the citizens, Kuniko goes to confront Nagiko about her role as first governor of Atlas. When she gets no answer, Kuniko has no choice but to banish her grandmother from Duomo. Before leaving, Nagiko informs her about Takehiko's disappearance after returning to the town. Miiko is forcibly turned into Hiruko's new vessel. Furukawa shares Kuniko his discovery that the artillery attacks came from a genetically modified plant called Daedalus. Ryoko also discovers this fact, but ignores the plant's threat as it will not be able to harm Atlas, but the same could not be said for Duomo and the rest living below. Kunihito makes his decision to leave the military. Mikuni pulls herself together and plans to attack Atlas to rescue Miiko. Kuniko and her team make their way to the forest to burn down Daedalus, but it retaliates against them. Mikuni fails to have her people kill Ryoko, but the woman brings her to see Miiko, who has turned into Hiruko's vessel. As Miiko's personality fights against Hiruko to speak with Mikuni, Ryoko has security surround Mikuni. Sayoko arrives to take Miiko/Hiruko hostage and leaves Atlas together with Mikuni. Momoko tells Kuniko that Daedalus will one day overwhelm and create a forest full of its plants, due to the bomb shower. As Kuniko contemplates this alone, Takehiko attempts to kill her.

Kuniko, Kunihito and Momoko go after Mikuni, who is about to make herself successor of Atlas. Kunihito distracts the guards with gunfire while the other two head in Mikuni's direction. Momoko fights off Sayoko, who attempts to stop them from reaching her mistress, leaving Kuniko to chase after the girl. Kuniko reaches Mikuni and tells her that she can be the successor, but all she wants is to activate the Zeus defense AI, but Sayoko knocks Kuniko down and tells Mikuni to keep moving. Mikuni reaches Ryoko and is told to present the three blade seals to her, though the girl have doubts due to Kuniko's explanation. However, Mikuni is told by Ryoko that she can only be successor if she gets rid of Sayoko. Even though Mikuni doesn't want to, Sayoko sacrifices herself by jumping to her death in order to make her the successor. When Mikuni and Sayoko enter the ceremonial hall, Kuniko grabs Mikuni with her and tells her that all she needs is to speak with Zeus. Upon interacting with a weird device which is used to activate Zeus, Kuniko realizes that Zeus cannot be controlled as she's not the successor. Ryoko reveals herself to be Zeus' avatar, and she easily beats down Kuniko. Despite Kuniko's pleas, Mikuni pushes ahead to destroy the world to avenge Mi-ko's death. When Kuniko tells Ryoko she will stop them, Kunihito appears, pointing his weapon at her.

Kuniko's arrival stops Mikuni from drawing the bejeweled spear and Ryoko states how impressed she is that Kuniko made it this far. She challenges Kuniko to pull the spear out herself. When Kuniko refuses, Ryoko takes Mikuni hostage and threatens to kill her, forcing Kuniko's hand and revealing that Kuniko and Mikuni are actually sisters and that their birth mother is no longer alive, but not exactly dead either. It is revealed that Kuniko and Mikuni were artificially created and that Kuniko is in fact a clone of Himiko, the mummy of the goddess discovered beneath Atlas. It turns out that Ryoko's body is failing her and she intends to invade the body of the new successor. Outside, a figure resembling Takehito expresses his disgust at the use of human lives to construct Atlas just before setting off a chain of chemical bombs. MEDUSA has gained complete control of the computer systems. Kuniko is forced to draw the spear in an attempt to stop MEDUSA from starting a nuclear war, but she's too late, as nuclear missiles are launched all across the world, launching incomparable amounts of dust into the already weakened atmosphere. MEDUSA himself predicts a nuclear winter with dropping water levels and temperatures everywhere and finally relaxes, convinced that he's safe at last. But his plans are breached when he opens the floodgates of the islands, thinking them useless and releases a tidal wave crashing toward him. It turns out that the missiles launched were a ruse to get MEDUSA's guard down and release the floodgates holding the water back. MEDUSA drowns in the rising floodwaters and Karin mourns his and her parents' deaths. Angered at the breach in her plan, Ryoko attempts to take over Kuniko, but Kuniko mocks her and a brief skirmish ensues, ending with Kuniko impaling Ryoko on the spear. Ryoko perishes and her life energy is absorbed by Zeus trying to revive Himiko. Sayoko appears in the catacombs, shaken but unharmed. Kuniko is carried away by the spear to the heart of Zeus where she meets Himiko, a duplicate of herself. Himiko plans to use all ten million citizens of earth to revive herself. Kuniko and Himiko face off, fighting for the future of the world. Kuniko's boomerang slices through the heart of Zeus, shutting the system down and banishing Himiko. Down in the catacombs, Miiko appears to Mikuni with the spirits of Hiruko and all of the sacrificed children. Miiko tells Sayoko to take care of Mikuni and then removes Mikuni's cursed power, as well as her illness. Karin laments the loss of her money, of MEDUSA and of her parents and Klaris and Zhang make their first appearances, claiming to have been worried about their friend, Karin. Karin brings out the microchip that was MEDUSA and it suddenly manifests as a miniature version of the previous program, which Karin reveals as MEDUSA's baby. It quickly recognizes her as 'mommy'. Zhang says that this time, they'll raise it properly. Atlas is destroyed and Kuniko and Kunihito gaze out over the horizon. Kuniko states her dream of creating a Shangri La.