Kuniko has a strange dream of Atlas, and learns from her grandmother, Nagiko, that her biological mother lived in Atlas. Takehiko and other Metal Age members raid a train from Atlas for supplies. Kuniko, Momoko and friends celebrate Miiko's departure to Atlas. Momoko entrusts Miiko with reopening the Tropical Fish, a bar staging Burlesque shows. Residents of Duomo get into an argument over Metal Age's responsibility for the attacks and their overall role. Kuniko wonders if everyone would be happy if they are able to live in Atlas, and makes a decision to go to the city. Karin is informed by her peer that she apparently messed with Saudi Arabia's carbon coefficient, thus making the latter rake in less money. She is confused by the apparent spike in the carbon economy. Ryoko's men find no new movements from the owners of the Sun and Moon blades. Kuniko, Momoko and Takehiko sneak into Atlas by faking identities as construction workers heading into the city. Miiko is forcibly recruited to be Mikuni's replacement retainer. Kuniko gets discovered while heading through a checkpoint in Atlas' support column and the group flees. They are chased by security, but fortunately an earthquake occurs and the group uses the distraction to escape. Kuniko wonders why everyone is not allowed to live in Atlas even though there were enough space to do so.

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.

Zhang continues to warn Karin of her country's status but Medusa limits his access privileges. Ryoko talks to Kuniko about the gas, but find neither of them involved with the gas attack. Ryoko threatens to blow the entire floor where Kuniko's forces are if they don't surrender, but Talsian offers protection for them if they agree to ceasefire. Kuniko shocks the rest by agreeing to the truce, as she doesn't want Metal Age to defy the orders of the United Nations and result in the isolation of Japan. As Metal Age give up their fight, Takehiko sees a ghostly white girl entering an old shrine inside the Atlas complex. He walks through a surreal landscape and finds his missing sister, Yasuko's shoes and cries. Karin discovers Zhang messing with her head leases and she vows to play his game and win. Kuniko secretly visits Atlas' residential area with Momoko but is chased by security. However, they end up trespassing Kunihito's mother's house and ask for help. Kunihito tries to look for his surviving mates on board the carrier and was told their records are not found. Karin is informed by Medusa that her company is now bankrupt. Nagiko is found to be assisting Zhang, who knows nothing of her identity, of the takeover in the leases. Karin sets Medusa to steal Atlas' treasury under Zeus' control. Talsian suggests reformatting Zeus, but Ryoko's group knows that once the AI is formatted, all critical systems will be shut down, and places him under arrest for suspicion of conspiring sabotage. Leon and his men arrive to arrest Karin but she manages to escape. Kunihito is shocked to see Kuniko and Momoko in his house with his mother, but does nothing. Later he returns Kuniko's old boomerang to her. Leon and his men goes to Mikuni's palace to arrest Miiko.

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.

Under the command of Kuniko and Kunihito, the bombers move into position and starts bombing Tokyo. Meanwhile, Atlas allows refugees from other regions to enter the city under close supervision and control from Metal Age members and Duomo citizens. Nagiko and Talsian reunite and play chess, as Nagiko realizes that Ryoko has become selfish and want control over Atlas instead of handing it to the Digmas. Karin continues making profits with the rising carbon coefficient while Akihabara is taking the brunt of the bombings with eveyone underground. Kuniko personally bombs Duomo, her old home, which is now gone forever. After confirming the complete purging of Daedalus infestations, the bombers return to base. Ryoko's men conclude that the only infestation left is in Atlas' eighth floor. Not only that, Japan is now the poorest country on the planet. Karin releases Medusa to claim the profits gained from the spiking carbon coefficient, but the AI goes out of control.

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.