It is the year 2201. The Yamato has returned from the devastating battle with Emperor Zordar and the Comet Empire. Sanada, Aihara, and Shima are released from the hospital, and go to pay their respects to the fallen crew members at Okita's memorial. They meet Tokugawa's son Tasuke, who says that he will be joining the crew once he graduates from cadet school. The next day at his graduation, he ends up capsizing a boat full of new cadets because they are all too busy staring at the Yamato to watch where they are going. 
After some problems during launch due to the new engine crew hitting the wrong switches and stalling the ship, the Yamato departs on what should be a simple training mission. 
(Source: AniDB)

A year has passed since the Star Force returned to save the Earth but another danger now approaches from deep space. A gigantic White Comet hurtles toward our galaxy, obliterating everything in its path. But it is no ordinary comet - it is the deadly Comet Empire, conqueror of worlds and Earth is the next target! Against orders, the Star Force blasts off to investigate, but even if they can get past the flagship Andromeda, they don't yet know the true nature of their new enemy!

The Black Nebula Empire attacks Earth and threatens to blow up the planet with a bomb they placed on Earth if counter attacked. Earths hopes rest on the Yamato crew as they go to the Black Nebula Planet and try to find a way to difuse the bomb before it's too late.
 
(Source: Anime News Network)

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