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.