Shangri-La

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.

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 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).

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.

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.