Hayato's peaceful life with his parents and his dog is brought to a dramatic, terrible end when a giant robot, said to be sent from a flying ghost ship, devastates the city, killing hundreds including Hayato's parents. Shortly before his death, Hayato's father reveals that he is not really their son. Hayato is now alone, struggling in this strange new world left after the disaster, where giant machines and monsters control the world. He sets on a dangerous quest to discover the mysterious powers that be, only to discover that he is directly connected to it all...

The Black Nebula Empire, last seen in Yamato: The New Voyage, lands a huge fortress on Earth and sends out an invasion force, with the Black Nebulan fleet wipes out Earth's space fleets. The fortress contains a bomb capable of destroying half the planet. The Nebulans threaten to use it if they are attacked. The Yamato reaches the other side of the Black Nebula and finds a grand, white galaxy, similar to the Milky Way. They follow a beacon signal to a planet that looks just like Earth. They land, and are greeted by an apparently human woman, Sada, and two officers from the Black Nebulan Empire. They meet the Emperor, Scaldart, who also appears to be a human. He tells them that they are actually back in the Milky Way, in the year 2402. The vortex was a hole in time. The Earth has been under Black Nebulan rule for 200 years, and he is the (puppet) governor. Scaldart shows Kodai and the landing party all sorts of collections of Earth's famous artwork, and, up on the Yamato, the video screen scans the surface of the planet to find all of Earth's famous landmarks...

The Comet Empire approaches, and the Yamato is ready to face them. But this will be the last battle for both sides. Susumu Kodai and Yuki Mori's wedding plans are postponed when the Yamato crew must report to take on another threat from the stars. A new enemy has 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.

Gamilons are a race of evil aliens that are trying to destroy the planet Earth. However, a group of civilians look to the battleship Yamato for its space travel and go on a mission to bring back a neutralizer that will get rid of the radiation from the Earth. Space Battleship Yamato (宇宙戦艦ヤマト Uchū Senkan Yamato), also known as Cosmoship Yamato and Space Cruiser Yamato, is the first theatrical movie based on the classic anime series (known as Star Blazers in the United States). Unlike the later films that would follow it, this is a compilation film consisting of various television episodes edited from the "Iscandar" arc of the television series. It originally had a new ending created for the theatrical release in which Starsha had died before the Yamato reaching Iscandar. This ending was removed for the television broadcast and was lost until the DVD release. In English speaking countries, it was known by the title Space Cruiser.