#1 - The Girl's Return

Season 1 - Episode 1

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.

#2 - Lipstick Cruelty

Season 1 - Episode 8

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.

#3 - The Creation

Season 1 - Episode 3

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.

#4 - Divine Prophecy of Sun and Moon

Season 1 - Episode 9

As the trio of Kuniko, Momoko and Tomoka watch the eclipse and destruction around them, Sayoko attacks them with her sniper rifle. While Momoko fights off Sayoko and her guards, Kuniko unknowingly attacks Miiko, but he manages to deflect her boomerang and recognizes who the owner is. Momoko falls prey to Sayoko's trickery and is taken away by the guards with an escaping Mikuni and Miiko, while Tomoka is slightly injured by a gunshot. Karin gets a call from Klaris who has gone bankrupt from the eclipse. She promises to give Klaris funds if only she helps her with a favor. A captive Momoko remains defiant against Sayoko, who recognizes a similar earring on him that Mikuni has as well. Ryoko reports to Hiruko about Kuniko and Mikuni, and a shocking secret of Hiruko's immortality is revealed. Kuniko returns home with Tomoka, but is upset about Momoko's capture. She struggles to rescue everyone with Takehiko and the others. Karin learns from Klaris that Talsian has ordered Medusa to infiltrate the Jupiter observation satellite. Medusa utilizes an orbital satellite to create typhoons on the ocean. Kuniko and Takehiko manage to dig out to the detention center, where they find Rena, Nao and all the prisoners dead. Kuniko breaks down and cries from her inability to save everyone.

#5 - Sad Thoughts of Love and Hate

Season 1 - Episode 7

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.

#6 - Flying Girl

Season 1 - Episode 13

Kuniko announces the beginning of Metal Age's fight for survival against Atlas government, for the sake of everyone. Talsian makes his first appearance as chairman of Atlas. Kuniko, Takehiko and Momoko go to what remains of Yokota Air Base to meet K.D., who will be providing Metal Age with a gigantic stealth bomber. Meanwhile, construction workers involved in the building of Atlas strongly oppose the inhumane treatment the people outside Atlas receive. The protest turns into a widespread riot against Atlas security. Under Kuniko's command, the stealth bomber carrying Metal Age forces approach Atlas, but are soon attacked by Atlas air force. Karin takes this chance to make money from the war. The air force fires missiles at the bomber but end up hitting Atlas' supports instead. Kuniko goes outside the plane to destroy the remaining missiles with her boomerang. Miiko teaches Mikuni a lesson in fighting for a cause. Under control of Zeus, Atlas sends multiple defense drones that attack both the air force and the bomber. As Kuniko and Momoko try to destroy the drones, the drones are in turn destroyed by the strange artillery strike that hit Duomo earlier. K.D. makes a suicidal attack on a drone after deploying Metal Age forces, who fly off in jet packs. Kuniko destroys the last drone and is rescued by Momoko. As Kuniko watches K.D. parachute himself to safety, she notices a hole in one of Atlas' supports created by an explosion that has disappeared.

#7 - Blade of the Sacred Sound

Season 1 - Episode 10

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.

#8 - Frenzy Wood Prison

Season 1 - Episode 16

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.

#9 - Tunnels on a Dark Night

Season 1 - Episode 17

In her safehouse, Karin finds out that all three Digmas have Atlas AAA ranks, which means they are highly regarded. Takehiko reveals to Kuniko that he was sent by Atlas to guard her. But he has decided to kill her and end Atlas' plans when he found out that they sacrificed children to build the city, including his sister. Kunihito arrives just in time to save Kuniko before Takehiko can kill her. Losing all hope, Takehiko tells Kuniko that AAA rank individuals will inherit Atlas, and he seemingly kills himself by jumping into a storm drain before Kuniko can stop him. Kunihito informs Kuniko that he has quit the army and will try to find his own way. Karin buys Akihabara as her "house". Mikuni and Sayoko arrive to seek refuge at Karin's territory, and place Miiko/Hiruko into a pool for safekeeping. Karin finds out the hard way in pleasing Mikuni. Kuniko and her team investigate the Metal Age's Nerima base, which has lost contact. They discover the entire Nerima base dead from exposure to photo-oxidants spread by Daedalus. Leon takes care of his brother Sion's injury caused by Ryoko's latest beating and tells him to quit if he doesn't like his job. But Sion tells Leon that he doesn't understand him. Kuniko goes to the three old otakus to buy a bomber, but is referred to Akihabara's newest leadership, Karin. Kuniko reveals that she wants to use the bomber to burn Tokyo to the ground, to Karin's shock.

#10 - Collapse's Prelude

Season 1 - Episode 23

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.

#11 - Shangri-La

Season 1 - Episode 24

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.

#12 - Straying and Defeat

Season 1 - Episode 15

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.