In the year 2202, Earth is suddenly attacked by the Black Nebula Empire. A massive fortress lands on the planet, and the empire’s fleet destroys Earth’s space defenses. The invaders announce that the fortress contains a weapon, the heavy-nucleon bomb, capable of destroying all life on Earth, and they will detonate it if the planet fights back. Facing total surrender, the Earth Defense Force is paralyzed.

Susumu Kodai, Yuki Mori, and the former crew of the space battleship Yamato gather in secret. They learn that the Yamato has been hidden and rebuilt on the asteroid Icarus. As they attempt to escape Earth to reach the ship, Yuki is wounded by enemy fire and left behind, captured by the Black Nebula intelligence officer Alphon. The rest of the crew reaches Icarus, where they reunite with the Yamato and its new commander, Captain Yamanami. Onboard, they meet a young girl introduced as Mio Sanada, the niece of the science officer Shiro Sanada.

The Yamato departs for the distant Black Nebula to find and destroy the bomb’s control system. During the voyage, Mio reveals her true identity: she is Sasha, the daughter of Kodai’s deceased brother Mamoru and the Iscandarian queen Starsha. Due to her Iscandarian heritage, she has grown to seventeen years old in only one year. Meanwhile, on occupied Earth, Yuki recovers under Alphon’s care. Alphon is drawn to her devotion to Kodai and, despite being an enemy officer, eventually reveals the bomb’s disarming method to her before letting her escape. Yuki joins the human resistance.

The Yamato crosses the Black Nebula and discovers a planet that appears to be an exact copy of Earth. They are welcomed by the empire’s leader, Scaldart, who claims this is Earth two hundred years in the future. He shows them a false history where the Yamato is destroyed and offers them sanctuary. The crew refuses the deception, and Sasha chooses to stay behind, believing she has a role to play. As the Yamato departs, Scaldart attacks, and the crew realizes the future Earth is a fake. Sanada deduces that the Black Nebulans are not future humans but cyborgs who lost their original bodies to automation and now seek to steal human bodies.

The Yamato turns back and fires its wave motion gun at the false planet, shattering the disguise to reveal the true mechanical world of Dezarium. Sasha contacts the crew from inside, guiding them to a vulnerable core. On Earth, Yuki confronts Alphon, who is mortally wounded. With his dying words, he explains that both the trigger on Earth and the control system on Dezarium must be disabled simultaneously. Yuki succeeds in disarming the trigger. Inside Dezarium, the Yamato’s bridge is hit; Captain Yamanami is killed, and the dying Sasha urges Kodai to fire the wave motion gun. Kodai obeys, firing into the core and destroying Dezarium. The bomb on Earth is neutralized.

As the Yamato journeys home, Sasha’s spirit appears to Kodai and the crew, blessing them before ascending. The ship returns to Earth, where Kodai and Yuki are finally reunited. The story explores themes of love, trust, and sacrifice across the separate struggles of Kodai and Yuki, with Sasha and Alphon serving as key figures in each character’s arc. The setting spans occupied Earth, the hidden asteroid base, and the strange double galaxy of the Black Nebula, culminating in the revelation of the artificial world Dezarium.