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.

The black dots raining down on Duomo lead to everyone fleeing, including Atlas security and military. After the attacks stop, Kuniko and the other Metal Age members perform a search and rescue operation of Duomo's residents. Lady Ryoko is furious on the unknown attack and Leon, one of her men, volunteers to bring a team to investigate the source. Meanwhile, Kuniko, Momoko and Takehiko decide to investigate as well, at the place the attacks supposedly originated from: Ikebukuro. Their team wears protective gear to protect from the dense oxygen and poisonous swamp gas. Karin works with several of her peers to control investments and economy of other countries. However, she goes into a bad mood when one of her peers posts a presumably sarcastic remark. Mikuni punishes one of her retainers for lying by killing her with her psychic powers. Kuniko's team encounter a military squad sent into the Ikebukuro jungle to investigate. They are discovered by Kunihito and flee. Kuniko ambushes Kunihito and interrogates him on the military's presence, and the resonance of their sacred blades. Kunihito claims not to know anything and Kuniko escapes. Ryoko's men find that the artillery attack emitted no carbon dioxide, leading them to wonder if it's nature's punishment on them. Atlas begins the regular ballot to allow Duomo residents to live in the city and Miiko is one of the chosen. Ryoko gets an audience with the lord of Atlas, telling him that the seals have resonated.

Karin convinces the Japanese government to use Kuwait as bait to lure out Serpent, despite the fact it will destroy that country's economy. Kuniko and Nagiko both watch the manipulation of carbon coefficient. Kunihito intends to resign for the loss of the mimic armor sample, but his superior tells him that Atlas has already pardoned him for this mistake. He is ordered to head for the Moon Palace to meet Mikuni. While Mikuni questions Kunihito on his recent events, Sayoko finds his Atlas rank is classified. She also discovers that his family blade matches the same material and shape as Mikuni's sacred blade. The lord of Atlas, Hiruko, goes hysterical from the thought of having the two blades meet. The government begins its hunt for Serpent. After Serpent takes the bait, Kuniko, with Nagiko's help, locates it originating from one of the islands in the Maldives. Ryoko obtains this information and sends it to America. Kuniko learns that America has dropped thermobaric bombs on the location, erasing Serpent's threat and stabilising the carbon market. Karin discovers it was her peer, Talsian, who created a copy of Medusa for the Maldives, using this incident to teach the original Medusa caution.

Atlas authority announces the imminent execution of Kuniko and everyone approach this news with mixed results. Momoko visits Kuniko in jail and hands her food prepared by Nagiko and a dress to wear before her execution. Tomoka reluctantly seduces the guard to allow her to talk to Kuniko but is caught by Leon. However, he lets Tomoka speak with Kuniko briefly before ending the conversation, telling her that he will pretend that the two girls' conversation never happened. Rena, Nao and the other prisoners plan something by bribing various guards or improvising various materials. Ryoko plans to do something about Kuniko and Mikuni's destinies with the former's execution. Wearing lipstick and her original colthes, Kuniko prepares for the execution. Suddenly, Kuniko cuts off the guards' weapons with nanowires from the lipstick and escapes with Tomoka on a hydrogen balloon the prisoners created, promising to come back for them one day. Ryoko is impressed by what Kuniko and the prisoners did, but she has the guards kill off all the prisoners. As Kuniko and Tomoka head home with a waiting Momoko, a solar eclipse occurs and Mikuni and her retainers play on the highway.

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.

Kunihito apologizes to Kuniko for his apparent betrayal, holding her off while Ryoko escapes to the Eternal Forest with Mikuni. Enraged, Kuniko attacks Kunihito, only to be stopped by Momoko who arrives to tell Kuniko of Kunihito's true motives. It's revealed that Sayoko survived her fall from the upper deck because Momoko intercepted her descent. Ryoko arrives in the chamber once occupied by Hiruko, revealing a hidden passageway into the bowels of Atlas itself. Shogo, Leon, and Sion attempt to stop her, but she eludes them and they descend down through the shaft. Sayoko is quick to follow. She voices Ryoko's motives in forcing Mikuni to become the successor. She attacks Ryoko, but is ultimtely knocked off the descending platform, presumably falling to her death. Nagiko and Talsian are seek talking about the hidden catacombs they discovered during Atlas's construction and the secret behind the forbidden relics they uncovered down there. The secret behind Zeus's creation is finally revealed, as well as the system protecting Atlas from violent oscillations and tremors. Back up in the ceremonial chamber, Kuniko and Kunihito finally manage to break through the barrier to the elevator shaft Ryoko took. Kuniko hugs Momoko and Kunihito apologizes for his actions. Kuniko playfully scolds him, saying he apologizes too much, before leaving down the shaft. Meanwhile, Karin is desperately struggling to stop MEDUSA's rampage across the economic markets. Talsian appears on the terminal and declares a way to stop MEDUSA. A rather comical chibi battle ensues and Karin is knocked into a separate field, greeted by the teddy forms of her parents, who reveal the real reason as to their extended absence. It's only a virtual program operated by Ryoko, but it turns out that Karin's parents had died three years before. Karin suffers a breakdown and Ryoko returns to reality to command Mikuni to draw the bejeweled spear and assume her role as successor. Mikuni, however, refuses, but after threats from Ryoko, obliges reluctantly. By now, MEDUSA is about to decimate the world's economy and Kuniko arrives just in time to stop Mikuni from pulling out the spear.

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.