In the year 2099, humanity comes under sudden attack by the Seireness, a mysterious race of giant life forms emerging from deep space. The assault results in over one billion deaths before the aliens inexplicably fall silent. Five years later, a young boy named Yu Yamato, who lost his mother Maya to the initial attack, turns twelve years old and sets his sights on joining the frontline base at Jupiter. He enrolls as a cadet for Topness, the Earth defense fleet organized to oppose the Seireness. As he struggles to pass his launch test and prove himself, the Seireness end their five years of silence and launch a new offensive, horrifying humanity once again with their beautiful yet grotesque appearance.

The story exists as a separate and distinct continuity from the original Space Battleship Yamato, taking place in its own original world with minimal overlap to the classic narrative. The protagonist Yu Yamato is an elementary school-aged boy driven by the loss of his mother. The enemy Seireness are portrayed as an unknown and terrifying force of nature rather than a conventional military opponent. The Topness fleet and its mecha designs were created by Junichiro Tamamori, a designer familiar to the franchise.

The narrative follows Yu as he faces the rigorous challenges of becoming a cadet, confronts the trauma of his past, and participates in humanity's desperate defense against the Seireness. The series was written and illustrated by Ryuko Azuma and ran for a total of twenty eight chapters, reaching its conclusion in August 2022. The collected chapters were compiled into five paperback volumes, with the first two released in April 2021, the third in October 2021, and the final two in November 2022.