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Season 1
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1. Return of the Girl
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.
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2. Cursed Sea of Ikebukuro
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.
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3. Creation of the Universe
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.
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4. Super Akihabara
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).
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5. Maddening Dance of the Tempest
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.
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6. Imaginary Battle Lines
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.
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7. Superficial Love and Hate
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.
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8. Lipstick Tragedy
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.
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9. Divine Sun and Moon
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.
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10. Soul Sword
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.
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11. Butterfly Visions
Karin sings a lullaby but doesn't remember how she knew it. Kunihito remembers the song while dreaming of obtaining the land blade when he was a child. He wakes up to find his remaining crew from the carrier adrift in the ocean. The carbon market is stabilized for the moment and Karin receives a cat for a visitor. Kunihito remembers that the carrier was enveloped by a light emitted from a satellite. Ryoko receives a report that their forces aren't able to close on Medusa's location due to typhoons. Karin receives a message from her parents that they will be back soon, however she laments that she's unable to leave the place, but a long-haired youth trespasses her place and invites her outside. Meanwhile the youth tries to get Karin to come out, but she vehemently refuses. She discovers that the guy wasn't captured by security on camera. Karin knows it wasn't a dream and wishes to see the guy again. True to her words, the youth reappears this time inside her room. He convinces Karin that she can interact with other people despite her protests. He invites her outside to a meeting, claiming she will find what she lost. Leon requests permission from Ryoko to view files pertaining to the Digmas. After days of waiting for help, Kunihito sees a plane headed in their direction. Karin finally leaves her home, which resembles a bird cage. She thanks the youth for helping her remember that her mother sang her the lullaby, and the youth disappears. Leon finds information pertaining to the youth, Digma Zero aka Canary, who supposedly died five years ago without having seen the outside world. As Karin finishes her song, the cat disappears as well. Kunihito as a child releases canaries from a bird cage.
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12. Creation of Mutable Elements
Kunihito recovers in hospital. Ryoko orders the survivors of the anti-Medusa operation besides Kunihito disposed of. She makes a press conference announcing the indefinite postponement of the Atlas Settlement Project. Metal Age is outraged and Kuniko decides to use aerial attacks on Atlas. Karin reaps a lot of money in her latest scheme and decides to go shopping outside. However, she wears a bear costume to cope with her fear of communicating with people. Sayoko barges into Ryoko's residence. Kuniko and Takehiko go shopping at Neo-Akihabara for tons of demolition materials and ammo. Ryoko informs Sayoko that the reason Mikuni has not been made successor is because there are two others, but she does not tell her their identities. Kuniko runs into Karin and talks to her, but the girl freaks out and flees. Sayoko tries to hack into Zeus, Atlas' computer system, but is thwarted by Ryoko. Miiko sees Sayoko being led away by Ryoko's men and he picks up Momoko's earring. Momoko wakes up to find herself released and finds her earring and a note from Miiko. As Kuniko and Metal Age plan to attack Atlas with all the forces they have, Momoko returns, to a very much relieved Kuniko.
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13. Flying Girl
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.