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.

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.

Karin attempts to keep Medusa under control but the building she's in collapses and she is forced to escape. Kuniko, Kunihito and Momoko arrive just in time to join in the rescue efforts to extract surviving Akihabara citizens. Kuniko talks some sense into a despondent Karin and join forces to prevent Medusa from causing the end of the world. They find the otaku owners, who have survived, to aid them in their operation. Using an independent network provided by the otakus, Karin hacks into the orbital communications satellite Icarus to send it descending onto Medusa's location. However, the celebrations are short-lived, as Medusa remains alive, tapping into the world military networks to prepare to launch warheads and create a nuclear winter. Karin reveals to Kuniko and Kunihito about their statuses as successors to Atlas. In order to use the Zeus AI against Medusa, they have to prevent Mikuni from becoming successor as the control system will only obey her commands. Mikuni ascends a long flight of stairs to Ryoko, who welcomes her to the Endless Forest.