A young girl, Kuniko Hojo, is released from the girls' detention center. She is picked up by her friends as well as her guardians, Momoko, Miiko, and Takehiko and returns to her home in Duomo. Kuniko is being groomed to be the future leader of Metal Age, a resistance organisation, which opposes the government's drastic policies on environmentalism. A high authority figure, Lady Ryoko, is informed of Kuniko's movements. Mikuni, a girl born from aristocracy, uses the highways of Atlas as her playground. Karin Ishida, a young computer genius, legally blackmails a politician from a 3rd world country into signing a banking contract with her company in Atlas, for overexceeding carbon emission. Takehiko recklessly burns fuel to celebrate Kuniko's return, in defiance on the government. The Atlas Security Corps and the military suddenly attack Duomo. Kuniko and the Metal Age members defend their town. They realise that Atlas is holding them responsible for an unknown incident. When Kuniko uses her boomerang on Major Kunihito Kusanagi, it hits his dagger, which causes Kuniko, Mikuni and Kunihito's sacred dagger to resonate. A moment later, mysterious black dots appear above Duomo and began raining down on everyone, causing mass destruction.

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.