While performing in a student film, Ataru cuts down Tarozakura, a large, ancient cherry tree. Strange things begin to happen all across Tomobiki: a mountain appears out of nowhere, spring changes to winter, and Lum loses her powers, while those around her act as if she doesn't exist.

The third film finds Ataru transformed into a pink hippopotamus, which sends Lum chasing after the wicked magician responsible, with catastrophic results. With Lum gone, her friends decide that there is no reason to remain, and so Tomobiki slowly returns to normal. The highlight of the film is a high speed chase scene with an angry Lum flying after the mysterious Ruu through the city at night and into a hall of mirrors (and illusion ). Ataru's true feelings for Lum are probably more obvious in this film than any of the others.

Time to ease up ... not! Although the Yamato's crew has witnessed the end of the long, hard-fought Comet Empire War, a peaceful future will have to wait. While Dessler gathers together the shattered remnants of his Gamilus Empire, new forces are at work in the universe that could augur in another conflict. Seems the Black Star Empire has invaded Dessler's homeworld and is decimating it, all the while gathering power for its war machine.

The Yamato and her crew face the onslaught of the Comet Empire, a civilization from the Andromeda Galaxy who seek to conquer Earth, led by Prince Zordar. They have harnessed a comet and is using its terrible power to unleash destruction upon its rivals and inferiors... which are in fact everyone. The Space Battleship Yamato heads back into action. But this time, it shall not return, and much of the Yamato crew have signed on for their last voyage.