In 2199, after five years of attacks by an alien race known as Gamilas, the Earth Defense Force launches 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 ship, 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 sacrificial lamb and tries to hit him, but crewmember Yuki Mori violently stops him.
Okita believes the hope for humanity lies within Iskandar. A request for volunteers for the mission is sent out, and Kodai - a former EDF pilot - decides to re-enlist. 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 of her admiration for Kodai, is bitter towards him.
The Yamato crew performs their first warp test and encounters more Gamilas ships. Since the Wave Motion Cannon is powered by the same reactor as the warp drive, the crew has to wait until the engine recharges before they can warp again. The Yamatodestroys 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 squad-mate, tells Yuki that Kodai left the service because he accidentally caused the death of his own parents and also Shima's wife during a mission.
After warping out of the Milky Way, the Yamato crew finds a Gamilas fighter adrift and recovers it to study, but 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 a race with a hive mind. Kodai stuns the possessed Saito, but the alien apparently is destroyed.
Later, an ailing Captain Okita makes Kodai the acting-captain. The crew discovers the captured Gamilas fighter 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. Kodai reluctantly orders Yuki, in her fighter, to blast the third bridge support away moments before it detonates, saving the Yamato but killing several crew. Kodai apologizes to Yuki for ordering her to doom their crew-mates, and they have an intimate moment as the ship warps again.
The Yamato arrives at Iskandar, but is met by a large Gamilas fleet that sends 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 crew thinks it is a trap, but Kodai urges them to go ahead. He leads an attack party to the planet's surface against heavy Gamilas opposition. Much of the assault force is killed, and the remaining pilots stay behind to cover for Kodai, 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 Earth as the most suitable replacement, after first killing off humanity. Iskandar did not agree with this and was imprisoned. Iskandar implants in Yuki the ability to clean the radiation from Earth. As she and Kodai return to the Yamato, Saito and Sanada sacrifice themselves by destroying the Gamilas power source. TheYamato returns to Earth, where Okita dies. The crew rejoices at their return home, but a surviving Gamilas ship ambushes them and severely damages the warship. Dessla now 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 his race. Kodai orders the surviving crew to abandon ship before he pilots the Yamato on a kamikaze attack against Dessler's ship. He fires the blocked Wave Motion Cannon, which destroys both spaceships.
The ending shows Yuki standing with a child, implied to be Kodai's son, on the Earth's surface now restored to its original state.
