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In the year 2199, the space battleship Yamato embarks on a voyage to the planet Iscandar, to retrieve a device that will rejuvenate a war-ravaged Earth.

2199 AD. Yamato tries 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 Dagam 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 is able to retreat, but ends up getting lost and finds itself in a strangely colored irregular dimension. The crew decides to turn off the ship's engine and explore a mysterious planet. In order to collect information Kodai, Kiryuu, Sawamura, Niimi and Aihara land on the planet. What they see when they arrive is a ship that's not supposed to be there. Dagam chases after the traces of Yamato's warp, and also reaches the strangely colored space. The planet where the crew of Yamato landed is in fact what Dagam has been looking for all along.