Sōji Ozuma commands the Great Yamato Zero, a warship initially dismissed as "the old wreck" by the Milky Way Alliance fleet. This vessel operates in 3199 as the A-Galaxy faces annihilation from the Seven Star Clan, the Metanoid Rakken, a massive force invading from a neighboring galaxy. With the Alliance reduced to only six operational fleets after devastating losses, Ozuma leads a crew assembled from diverse subterranean human cities. These members bring unique traditions and perspectives but unite under his command to protect the A-Galaxy.

Ozuma's leadership proves critical as the Great Yamato Zero undertakes missions supporting the decimated Alliance. His decisions, the bravery of crew member Shinma Oki, and the wisdom of scientific team leader Toshizō Iga become pivotal in uniting the crew and engaging the enemy. Throughout the conflict, the ship's hidden capabilities and technological secrets are gradually revealed to Ozuma and his crew, influencing their strategic choices during battles. A significant challenge arises when they confront the Metanoid Rakken's 20-kilometer-long flagship from the Draco constellation, a vessel designed to destroy planets by extracting their magma.