In 2199, after years of attacks by alien Gamilas which rendered the surface of Earth uninhabitable and forcing humanity underground, the people of the Earth Defense Force launch a counter-offensive near Mars. The fleet's weapons are no match for the Gamilas, who easily wipe out much of the force. During the battle, EDF captain Mamoru Kodai volunteers to use his damaged ship, the destroyer
Yukikaze, as a shield to cover Captain Jyuzo Okita's battleship, allowing his escape. Mamoru's ship is destroyed. On Earth, Mamoru's brother Susumu is scavenging on the irradiated surface near the half-buried wreck of the
battleship Yamato, when an object impacts near him and knocks him unconscious. He awakens to find an alien message capsule. Susumu also notices that the
radiation has been reduced to safe levels around him. He is rescued by Okita's returning ship and it is discovered that the capsule contains engineering schematics for a new warp drive and coordinates for the planet from which it came, Iskandar. After learning what happened at Mars, Susumu accuses Okita of using his brother as a living shield and tries to hit him, but crew member Yuki Mori violently stops him. The radiation that covers the Earth's surface is slowly sinking into the ground, and the scientists predict that the human race will become extinct in one year. Okita believes that the hope for humanity lies at Iskandar. A request for volunteers for the mission is sent out, saying that Iskandar possesses a device that can remove the effects of radiation. Kodai - a former EDF pilot - decides to reenlist. Their last battleship, the long-dead
Yamato, is rebuilt and enhanced with alien technology. Before the
Yamato can launch, the Gamilas attack with a gigantic missile. Captain Okita gives the order to fire the yet-untested Wave Motion Cannon, which successfully destroys the incoming missile. Kodai is reunited with his old fighter squad. Yuki, who joined the EDF years ago because she admired Kodai, is bitter towards him, believing he left out of fear. The
Yamato crewmen perform their first warp test and encounter more Gamilas ships. Since the Wave Motion Cannon is powered by the same reactor as the warp drive, the
Yamato crewmen have to wait until the engine recharges before they can warp again. The
Yamato destroys the alien capital ships, but the battle damages Yuki's fighter. Kodai launches to rescue her and is sent to the
brig for disobeying orders. Shima, Kodai's former squadmate and Yamato's navigator, tells Yuki that Kodai left the service because he accidentally caused the death of his own parents and also nearly Shima's pregnant wife during a mission. After warping out of the Milky Way, the
Yamato crewmen find a Gamilas fighter adrift and recover it to study. At the same time, Captain Okita goes into
cardiac arrest and is revealed to be terminally ill. However, the alien pilot is still alive and possesses Commando Team Leader Hajime Saitō, in order to communicate. The alien calls himself Dessla and says the Gamilas are the racing aliens with a
hive mind. Kodai stuns the possessed Saito and the alien apparently is destroyed. Later, an ailing Captain Okita makes Kodai the acting-captain. He also reveals that the capsule contained only the plans for the Wave Motion Engine and the coordinates to Iskandar, and the idea of the device was made up to give humanity hope. The
Yamato crewmen discover the captured Gamilas fighter which contains a homing beacon, giving away their position. The
Yamato fires its Wave Motion Cannon to destroy a Gamilas ship, but a stealth Gamilas spacecraft latches onto the ship's occupied third bridge on the bottom of the hull and begins a self-destruct sequence. Kodai reluctantly orders Yuki, in her fighter, to blast the third bridge support away moments before it detonates, saving the
Yamato but killing several crewmates. Kodai apologizes to Yuki for ordering her to doom their crewmates, and they have a romantic moment as the
Yamato warps again. The
Yamato arrives at Iskandar, but is met by the Gamilas from the large fleet who send a spacecraft to obstruct the muzzle of the Wave Motion Cannon. With their main weapon disabled, Kodai makes the dangerous choice to conduct a random warp and ends up at the opposite side of Iskandar. They are surprised to see that it is lifeless, and in fact strongly resembles Earth in its presently irradiated state. It is then discovered that Gamilas and Iskandar are the same planet. The crewmates of the
Yamato think it is a trap, but Kodai urges them to go ahead. Kodai leads an attack party to the planet's surface against heavy Gamilas opposition. Much of the assaulters are killed, and the remaining pilots stay behind to cover for Kodai, science officer Sanada, Saito and Mori as they head for the coordinates. Once they reach the coordinates, an alien possesses Yuki's body and explains that the Gamilas and Iskandar are two aspects of the same race. The alien says their planet is dying and they saw the Earth as the most suitable replacement, after first killing off humanity. Iskandar did not agree with it and so they were imprisoned. Iskandar implants in Yuki the ability to cleanse the radiation from Earth. As she and Kodai return to the
Yamato, Saito and Sanada sacrifice themselves by destroying the Gamilas power source, destroying most of the Gamilas forces. The
Yamato returns to Earth, where Okita dies. The crewmen of the
Yamato rejoice at their return home, but a surviving Gamilas ship ambushes them and severely damages the battleship, disabling all of its weapons. Dessla appears and says they no longer wish to invade the Earth. However, since the majority of the Gamilas were killed, he intends to destroy the planet with his ship to avenge the racing Gamilas. Kodai orders the surviving crewmen of the
Yamato to abandon ship before he pilots the
Yamato on a
kamikaze attack against Dessla's ship. He fires the blocked Wave Motion Cannon, which vaporizes both spaceships. The ending shows Yuki standing with a child, Kodai's son, on the Earth's surface which is now restored to its original state. ==Cast==