Gamilans are facing their biggest hurdle yet: their planet is dying at an alarming pace. To save his people and relocate them to habitable land, Aberdt Desler feigns submission to the oppressive rule of the planet Galman, which houses a race almost identical to the Gamilans. Desler's true objective is to seize control and accelerate the salvation of his nation. However, as Gamilans begin their migration, an unidentified massive power attacks them and completely warps their twin planet—Iscandar, Queen Starsha's home.

Meanwhile, Earth is celebrating the success of the magnificent Space Battleship Yamato and its heroic crew. A new generation of promising recruits joins Yamato and its two new support ships, led by Yuki Mori and Shirou Sanada. But not everyone agrees with the past decisions of its captain, Susumu Kodai. During the Yamato's six-month-long training mission and diplomatic meeting with the Gamilans, the crew learns of the recent catastrophe, and against all orders, Kodai commands the fleet to Iscandar to aid the surviving refugees.