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.

Three years since the return of the legendary Space Battleship Yamato, Earth has begun rebuilding itself and has made peace with the Gamilans. However, this recovery comes at the cost of utilizing the forbidden Wave Motion technology. Meanwhile, the notorious former crew members of the Yamato, who have each gone their separate ways, receive a psychic message from the mysterious Goddess Teresa. She urges them to return to their beloved ship and travel to the distant planet Terezart. They are promised a revolutionary power to combat the unprecedented threat of the relentless Gatlantis Empire, who are approaching Earth with all but innocent intentions. Unable to resist her plea, the crew reassembles and sets sail on another perilous intergalactic voyage, one that will test their sheer courage and versatility in the face of an even greater foe.

Earth's once green hills and rich blue oceans have been converted into a desolate wasteland by the relentless onslaught of planet bombs from the expansionist Gamilas Empire. By the year 2199, humankind has retreated to the depths of underground cities to escape the radiation. However, all hope is not lost, as the distant planet Iscandar offers Earth its final salvation: the Cosmo Reverse System, capable of restoring Earth's irradiated surface. In a desperate bid to retrieve this technology from Iscandar, the Earth Defense Force pours its remaining resources into the Yamato—an innovative, state-of-the-art battleship equipped with an infinite energy Wave Motion Engine. From young talent such as Tactical Officer Susumu Kodai to accomplished veterans like Captain Juuzou Okita, the Yamato's crew consists of many individuals, all varying in their experience on the battlefield. But despite their differences, one goal unifies them all: to complete their perilous 168,000 light-year voyage to Iscandar and save humanity from imminent doom.

2199 AD. Yamato tried to leave behind the Large Magellanic Cloud galaxy, after receiving a "Cosmo Reverse System" at its destination, Iscandar. However, suddenly, it encounters a mysterious group at the edge of the Large Magellanic Cloud. The crew finds out that the group is called the "Gatlantis," and that its leader is the Gutaba expeditionary force commander who calls himself "Goran Dagaamu of Thunder." The commander demands that Yamato be handed over to him. Yamato, wanting to hurry to Earth, escapes the fray. However, Yamato is attacked by a devastating beam weapon called the "Flame Direct Attack Cannon" that can transcend space. Yamato was able to retreat, but ends up getting lost, and finds itself in a strangely colored irregular dimension. The crew decides to turn off the engine on the ship, and explore a mysterious planet. In order to collect information, Kodai, Kiryū, Sawamura, Niimi, and Aihara land on the planet. What they saw when they arrived was a ship that was not supposed to be there. Dagaamu chases after the traces of Yamato's warp, and also reaches the strangely colored space. The planet on which Yamato landed was in fact what Dagaamu had been looking for all along. (Source: ANN)