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 starship Yamato is launched from a secret base and tasked with finding the Black Nebulan home planet, from where the bomb is controlled.
The Black Nebula is a double spiral galaxy near the Milky Way. The disc facing Earth is made of black, inert matter obscuring all light from the other disc, so the galaxy has never been seen before.
There are three new crew members. Shiro Kato, the original Kato’s (who died in Yamato 2) younger brother. Sasha is the daughter of Starsha and Mamoru Kodai, and has grown from an infant to a teen in only 1 Earth year. The third new member is Captain Yamanami.
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.
Scaldart shows them a time viewing machine which shows the history of the Yamato from 2199 up until the present. Then he shows them the future. The Yamato, orbitting the Earth, is destroyed by the enemy’s flagship, the Grodaze, in 2402.
The landing crew returns, demoralized, to the Yamato… except for Sasha who seems to know her true destiny. She abandons the party and remains on conquered Earth. while alone on the surface, her mother Starsha appears in a vision. She tells Sasha that she was born between Iscandar and Earth, and that her destiny is to die far from both, in service of both.
In orbit, the Yamato is attacked by the Grodaze and its fleet, with Beta particle guns firing on the ship. But the Yamato isn’t destroyed as predicted. Sanada surmises that the people the planet was not really human and all of the artwork used as proof were fakes. Could the Earth below them be fake, too?
The Yamato fires its Wave Motion Gun at the Grodaze and its fleet, destroying them. But, the tachyon based energy of the Wave Gun has an unexpected reaction with the beta particle energy from the exploding enemy ships. A huge explosion hits the Earth, destroying much of the surface. The Earth, where Sasha remained, dissolves in fire.
The fire reveals the black skeleton of a planet. It is not Earth, but the Black Nebulan home planet of Dezarium. It was an elaborate hoax designed to demoralize and defeat the Yamato. Scaldart pulls off the mask he wore to reveal his true Black Nebulan face.
Back on Earth, Lt. Arufon frees Yuki, who leads an assault on the fortress. She has a showdown with Arufon, but he is shot by another Earth trooper. Arufon tells her that his people are a race of cyborgs, who gave up their flesh for longer lives as Mechanisms. But they also lost the ability to love in the process. Arufon gives Yuki the plans to the fortress, including instructions on how to disarm its hyperion bomb, and dies in her arms.
Sasha manages to survive the incineration of the surface by escaping to the planet’s lower levels. She finds a control center and sends a message to the Yamato, telling them that to destroy Dezarium, they must travel to the core through a huge conduit she is about to open. Scaldart announces after her message that if the Yamato proceeds any further, he will detonate the hyperon bomb on Earth.
Yuki’s radio message interrupts Scaldart, telling the Yamato that she is alive, the invaders and their fortress have been immobilized and that the hyperion bomb has been disarmed.
The Yamato speeds though the conduit, dodging all sorts of enemy fire. It reaches the center of the planet where it finds a huge crystal city, looking like a glass sea urchin. The Yamato is hit by a missile and Captain Yamanami is killed. Kodai prepares the Wave Gun, but stops when he realizes this will also kill Sasha. Sasha again radios the Yamato, insisting that they fire since this is her destiny. Scaldart finds and shoots Sasha. An enraged Kodai fires the Wave Gun.
The blast sets off an explosive chain reaction. The Yamato does a 180-degree turn and rushes out of the internal chamber, going to emergency warp when it reaches the conduit exit. Dezarium explodes behind them, destroying the delicate gravitational balance between the two sides of the Double Galaxy. They crash into each other, starting the birth of a new galaxy.
The Yamato warps home while Yuki looks towards the glowing horizon for their return.