In the year 2220 A.D., the Earth Federation launches a plan to evacuate Earth when discovering that a traveling black hole capable of destroying anything in its path is on course towards the solar system. As the people on Earth prepare to relocate to planet Amare, whose ruler offers refuge, the tyrants known as the "S.U.S. Empire" attack the first Earth evacuation fleet. After learning that his wife Capt. Yuki Mori-Kodai disappeared in the battle and that legendary space battleship Yamato has been fully rebuilt, Susumu Kodai accepts command of the ship as he intends to not only help humanity once again, but also find Yuki in the hope of helping his relationship with his daughter Miyuki, who puts the blame on him for her mother's disappearance. But in order to fullfil the mission, the Yamato must go through battles against the SUS Empire, who intend to spoil humanity's hopes of finding a new place to live in and turn Earth into energy for their own selfish needs.

The battle with the White Comet Empire, Yamato finally returns to Earth to obtain more members and be inspected for repairs. When he returns to his home planet, Desler, but instead he finds the fleet of the Black Nebula Empire strip mining the Earth for its core. During a seemingly standard training mission a month after the war with the White Comet Empire, the crew of the Yamato face a new enemy: the mysterious Dark Nebula Empire. Kodai, Shima, Yuki, and the rest of the ship's crew have to ally with ex-enemy Desslar in order to foil the Dark Nebula's plans of strip mining Iscandar - the home planet of old friend Starsha, who helped the crew during their first voyage. Yamato: The New Voyage (宇宙戦艦ヤマト 新たなる旅立ち Uchū Senkan Yamato Aratanaru Tabidachi, lit. "Space Battleship Yamato: The New Journey"), also known as Bon Voyage Yamato, is a 1979 Japanese animated television movie that was first broadcast on Fuji TV. This was the third movie in the Space Battleship Yamato saga (however, Be Forever Yamato is the third theatrical movie). The Yamato crew must defeat the new Dark Nebula Empire. This film is the first in a two-part story arc that continues in Be Forever Yamato.