The year is 2205. Dessler, in search of a place for the Garmillas people to emigrate to, arrives at a planet named "Galman". Meanwhile, on Earth, the 65th Escort Squadron is born, with the Space Battleship Yamato as its flagship. Among the young crew members who spend their days training before departure, there is a young man, Domon Ryusuke, who turns a steely gaze toward the Yamato.

Domon had obtained his assignment to Yamato through illegal means. The day of the 65th convoy's departure. The Yamato is set in motion by a new crew. In the engine room is Tokugawa Taisuke, the son of the chief engineer Tokugawa. And at the helm is Domon. Susumu Kodai, now Yamato's captain, questions his resolve by entrusting the ship to him.

Countless black spears (Detherium Hammers) suddenly appear and stab into Garmillas, accelerating the melting of the planet's core. The planet begins to collapse, the earth is torn apart, and the remaining people are swallowed up by the magma. Dessler's determination to save as many people as possible is in vain, and now the final hour has come for Garmillas...?

The Dezarium Fleet Attacks! In order to save the refugees who had evacuated to the sea of Iscandar, the Dessler fleet continued to fight in isolation. However, the Earth government, fearing that the war might escalate, forbids Yamato to intervene and orders it to return home. Unsatisfied with the attitude of the adults, Domon and the other youths plot a rebellion.

The Yamato and two of its ships reach Iscandar, where they are joined by the Dessler fleet. Dezarium is targeting the planet Garmalio in the Bolzon solar system as an energy resource to further warp Iscandar. In order to frustrate this plan, Kodai decides to destroy Garmalio with a wave motion cannon.

The Earth-Garmillas fleet, helpless in the face of Dezarium's Autoplanet Gorba, decides to give priority to the rescue of everyone on Iscandar. However, Kodai, feeling guilty about the use of the wave motion cannon, is adamant about persuading Starsha. Dessler hurls words of contempt at her.

Starsha invites Kodai and Dessler to Sanctel, a sanctuary which extends beneath Iscandar. In the great repository of star elements, Kodai is reunited with his late brother, Mamoru Kodai. What is the truth of Iscandar's "salvation" that brings peace to all intelligent life, and what is the truth of Garmillas?