In a dystopian future, Earth is under siege by an alien race known as the Gamilas, whose relentless attacks have rendered the planet's surface uninhabitable. The remnants of the human population are forced to live underground, struggling for survival. In a glimmer of hope, an ancient spaceship called the Yamato is discovered buried beneath Earth's surface. The ship is equipped with advanced technology and a mysterious warp drive. The International Military Spaceship Force, led by Captain Okita, decides to restore the vessel and embark on a perilous journey to a distant planet called Iscandar. The mission's goal is to retrieve a device that promises to cleanse the radiation contaminating Earth.

Aboard the Yamato, the crew faces various internal and external challenges, including space battles, personal vendettas, and moral dilemmas. Kodai, a skilled pilot with a tragic past, becomes a central figure in the mission and grapples with his inner demons while forging bonds with fellow crew members like the determined Yuki and the veteran Shima. As they navigate through uncharted territories and hostile encounters, the crew's resilience and unity are continually tested. Their journey is filled with high-stakes decisions that determine not only their fates but also the future of humanity itself.