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For their silver anniversary, Vanilla and Coconna return to Uoodo along with Gotho in the hopes of reuniting with Chirico. Once there they find a red shouldered AT at the Battling arena.

In the Republic of Kumen, where conflict continues to this day, the government president and his guards, under pressure from the coup d'état forces, are abandoning the capital and fleeing. The president is none other than Kiriko's comrade-in-arms, Potalia. Vanilla and her friends arrive in Kumen in search of Kiriko, and thanks to Goto's help, they enjoy a one-night revival of the "Phantom Club." Cocona dresses up as a diva, former regulars... And an invitation has also been sent to the fugitive president.

Sandstorms still rage on the planet Sansa. Kiriko has been living in Zoffy's scrap metal shop for three months, cutting steel beams from giant battleships. Zoffy has lost her eyesight after a long and harsh life, and she never imagines that the young man caring for her is Kiriko, whom she once hated as her enemy. While Kiriko is away, Zoffy's office is suddenly attacked by ATs. Kiriko realizes that this is a plan to make Zoffy a hindrance, but he carries her on his back and walks through the desert.

Falling beneath the temple, Kiriko and Le Shakko come face to face with an underground tree, the underground stem of Gomoru Tower. They fend off the temple's ATs, but suddenly a mysterious creature entangles them in its cocoon threads and takes the baby from them. Juno, who was once cast away as the child of God, appears and saves the pair, who are unable to move. Together with Juno, they try to retrieve the baby, but the god of Nurgelant has prepared various trials for Kiriko that will dig deep into his memories...

As the Gilgamesh and Balarant fleets stare down the planet Nurgerant, Pope Montewells enters the Tower of Gomor. The Pope meets the former god Wiseman, who has repaired himself over time, and asks to be entrusted with the upbringing and guardianship of the god's child. Meanwhile, Kiriko breaks through the Underground Tree and is invited into the space where Wiseman and the baby are sitting. After 30 years, the fateful showdown between Kiriko and Wiseman begins again...