Kuniko muses on the vision of Atlas, and decides to finance a rebellion against Atlas by selling the community's store of graphite (which is rich in carbon). Escorted by Momoko (over Takehito's objections), she travels to the black market in Neo-Akihabara, a place still populated by electronics shops and otaku, where she encounters many colorful figures, some of them relics of our own time. In Atlas, we learn that Miiko has become a trusted retainer for Mikuni. Meanwhile, Karin and her companions become aware that someone else is manipulating the carbon market. Karin concludes that to do so, this other party must have duplicated their computer system, and she focuses her own search on Akihabara. While searching there, she notices Kuniko (seen through a security camera).

Ryoko's men launch a sneak attack on Duomo, demanding Kuniko to come with them. Tomoka gets herself involved and is taken along with Kuniko. Both girls are taken to the detention center from witch Kuniko was previously released. Ryoko has taken the position of prison commandant to watch over Kuniko. Kunihito wants to question Kuniko but is told by his superior that she is held under custody by Atlas authority. Kuniko is constantly bullied by Rena and her gang, who appeared in the center after Kuniko was released. After defending a friend from being threatened, Kuniko learns that Rena bullies her in order to obtain an Atlas rank offered by Ryoko. Kuniko gets into a fight with Rena and defeats her, but she takes the blame for her when Ryoko punishes Rena for failing in her mission. Kuniko spends the next three days standing without food and shelter under the sky. Tomoka reveals to Rena that Kuniko took the blame for her actions and ended up in the detention center two years ago. On the 3rd day, Ryoko is impressed by Kuniko's endurance and offers her a present, saying that she will execute her. At this, Kuniko finally breaks down and loses consciousness.

Karin tells Kuniko that she won't be able to sell her so many resources to combat the Daedalus, but she will be able to rent them to her. In exchange, Karin wants Kuniko's sun blade. When Karin recognizes Momoko's earring, she is forced by Momoko to bring her and Kuniko to the other owner of the earring, which is Mikuni. After both sides explain how they got their earring, Kuniko and Mikuni are faced with the prospect that they are sisters. Momoko and Kuniko are also led to the pool to see Hiruko, with Mikuni telling them that Mi-ko is the new vessel for the spirit. Back in Duomo, Kunihito tells Kuniko that the Daedalus has begun to spread in the town and Atlas as well. As Metal Age discuss their options to evacuate Duomo, Nagiko returns. Kuniko questions her grandmother's motives, but she tells the girl that she will need her help in dealing with Daedalus. In exchange, Nagiko wants Kuniko to accompany her to see Ryoko. Kuniko will burn the Daedalus down, in exchange Ryoko will have to allow Duomo and other refugees residence in Atlas. When Ryoko refuses, Kuniko has Kunihito cause an explosion, attracting Daedalus to attack the main power grid. With Kuniko's threat, Ryoko says she will aid her in destroying Daedalus.

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.