Space Battleship Yamato 2199

In the year 2199, Earth is ravaged by attacks from alien beings of the planet, Gamilus, which have devastated the surface of the Earth and forced what remains of mankind to take shelter underground. To save the Earth, the last of the Earth's space forces must distract the Gamilan forces while a non-Gamilan ship, code named "Amaterasu", races to Mars to deliver the Wave Motion Activation Core to the Earthlings. While Captain Mamoru Kodai contains the enemy attack to allow fellow captain Juzo Okita to escape with his forces, Mamoru's brother Susumu and his friend Daisuke Shima investigate the "Amaterasu" that crashed on Mars. Inside the wreckage there is a deceased alien female, the lone messenger sent to Earth to make a critical delivery to the Earthlings. Susumu and Daisuke return to Earth on the Kirishima, their only ship to return from the battle at Pluto. On the Kirishima, Susumu learns of his brother's death. When the Kirishima reaches Earth, Susumu Kodai looks for Captain Okita to confirm whether his brother was sacrificed in vain and meets Yuki Mori, who directs him to the hospital wing. Kodai confronts Okita, who claims responsibly that it was he who led Mamoru to his death.

Susumu brings the Wave Motion Activation Core to Earth which allows mankind to complete its first interstellar spaceship, the "BBY-01 Yamato". With Okita as the captain, Shima as the navigator, and Susumu as its tactical officer, the Yamato is commissioned to travel to planet Iscandar, in the Great Magellanic Cloud, with orders to retrieve a device able to restore Earth's environment. Before the Yamato can start its journey, it must counter an inbound Gamilan interplanetary ballistic missile targeted at them.

On Gamillan occupied Pluto, Gantz suggests sending out a fleet after the Yamato. Schultz turns down the suggestion, preferring to see what the Yamato does before attempting anything. After making an interrupted space warp, the Yamato 's main engine malfunctions, so Captain Okita orders the Yamato to land on a floating continent orbiting Jupiter, to make repairs. On the floating continent, Captain Okita orders an away team to go out and collect samples from the continent. After analyzing some of the plant samples collected, XO Shiro Sanada discovers that the floating continent is artificially made by the Gamilans. Meanwhile Raleta, commander of the Gamilas resupply base on the floating continent, gets a message from Gantz, ordering her to dispatch a combat fleet of four ships to attack the Yamato. The Yamato destroys three of the four attacking ships, and then takes off from the continent. Okita orders Kodai to test fire the Wave Motion Cannon at the floating continent. Nobody is certain of what would result. Kodai fires the gun, destroying the entire continent. Nanbu is thrilled at the power of the weapon, but Okita forbears that the Yamato 's weaponry is for self-defense only, questioning whether they have done the right thing.

When the Yamato lands on the Saturnian moon of Enceladus to mine some much needed cosmonite and investigate an automated distress call. Susumu, accompanied by radar operator Yuki Mori and a medic, encounter the remains of a crashed Earth ship. They are ambushed by androids sent by the Gamilans and must fight to escape. In the chaos of battle, Susumu fumbles his sidearm but quickly scounges up a pistol which upon closer inspection finds it to be his brother's. He uncovers the vessel's exterior markings, the Yukikaze. Unable to find any further clue about Mamoru's whereabouts, they plant the Yukikaze's memorial marker and continue their quest.

Before leaving the Solar System, the Yamato launches an attack to destroy the Gamilan facilities on Pluto to stop their bombardment of Earth with planet bombs. However, the ship ends up falling for a surprise attack from the enemy's secret weapon, and the crew of Yamato sends their pilot squadron to shut down the Gamilan base.

Having deceived the Gamillans to believe that the Yamato was destroyed for sure, the ship takes the opportunity to stage a counterattack after the recon pilots find the location of the main Gamillan base. The destruction of the base puts an end to radiation bombs falling on Earth, and Earth forces thank the crew for that.

With the Gamilan attacks on Earth stopped, the Yamato prepares to leave the Solar System after giving to the crew members a last chance to contact their relatives they left behind before resuming their journey to Iscandar. The last calls are often upsetting to the crew.

An operation staged by the Gamilan Leader, Abelt Dessler, forces the Yamato to navigate too close to a star in a desperate attempt to escape, maneuvering around solar flares that can instantly destroy the ship while being pursued by the enemy forces who are seeking redemption for the destruction of their Gamilan base on Pluto.

One of the Gamilan androids retrieved by the Yamato on Enceladus is reassembled and activated in an attempt to learn more about their enemies. Analyzer, the Yamato's own robot, develops a rapport with the android. As the android secretly explores its surrounding medium, it encounters a mysterious entity. Analyzer manages to befriend the Android which then reveals its meeting with the shipboard "goddess". However, when the android escapes its confinement, the rest of the crew enters an alarmed state of alert and searches for it.

The Yamato falls into a dimensional rift and finds itself unable to escape. A Gamilan ship that is also trapped there approaches the Yamato and both crews come to a temporary ceasefire while they work together to escape. Lower Storm Leader Melda Ditz, the daughter of a senior Admiral in the Gamilas fleet, remains on the Yamato as part of the agreement. After the Yamato escapes the dimensional rift, General Goer charges at them with a Gamilan fleet. Instead of fighting this fleet, the Yamato runs away, and the dimensional rift temporarily reopens, swallowing much of the fleet. Ditz is now trapped on the Yamato.

Melda Ditz, a Gamilan pilot under the custody of Yamato, is given a medical examination by Dr. Sado and is found to be identical to humans at the DNA level, except for the blue skin. She claims that their attack on Earth was not unprovoked, and that it was the Terrans who first fired without warning during the first contact between both races years before. Daisuke, whose father was killed in the attack, does not believe her at all until Yamazaki, the sole survivor of his father's ship, reveals to him the truth about what really happened that day. At the end, Ditz is given four days of food supplies and leaves the ship on friendly terms.

General Domel of the Gamilans is called back from the front lines by Dessler and reassigned to the Milky Way with orders to stop the Yamato. As the Yamato approaches the edge of the galaxy, the crew comes under attack by an extra-dimensional submarine.

Taking shelter in an asteroid cluster, the crew of the Yamato discover the enemy's ability to hide their vessel in sub-space and come up with countermeasures against them.

Returning from a reconnaissance mission, Kodai and Yuki find a drifting Yamato with the rest of the crew missing. As the two look for clues about what happened, they must face an enemy that can use their own memories against them, assisted by an unexpected ally.

General Domel devises a scheme to trap the Yamato in the midst of a massive fleet of Gamilas warships, but he is unaware of what is taking place behind the scenes on his homeworld.

Badly damaged and in need of provisions, the Yamato lands on a lush, fertile planet named Beemela. As a ground team makes a startling discovery, there are doubts if the ship still has a chance to complete its journey in time and the security force attempts a mutiny.

With the aid of an alien device, Kodai, Yuki and Sanada explore the control center of an abandoned warp gateway created by an ancient civilisation under Gamilas control. In the midst of a deadly undertaking, Sanada unveils a surprise about the Yamato 's navigational functions and his close friendship with Kodai's late brother, Mamoru.

Using the newly reactivated warp gateway, fighter pilot Shinohara scouts the intended shortcut to the halfway point at planet Balun. Once there he discovers a vast fleet of over 10,000 Gamilas ships. However, Okita declares that the Yamato must fight its way through the enemy's massive armada if they want to reach the Large Magellanic Cloud in time.

As the Yamato penetrates the Large Magellanic Cloud, Domel, his name now cleared, engages in a battle of wits with Okita as he prepares a special attack force to stop the Earth vessel once and for all.

Domel's task force engages the Yamato in a nebula dubbed the Rainbow Star Cluster. During a fierce battle in which the Yamato is heavily damaged and its Wave Motion Gun disabled, it is infiltrated by Gamilas operatives tasked to kidnap Yurisha of Iscandar.

Yuki is taken to a Gamilas prison colony called Leptopoda. The Yamato is not far behind, its crew unknowingly seeking to resupply and repair. During a recon mission, Kodai and several others are also taken prisoner just before an old acquaintance foments a riot.

Okita's condition takes a turn for the worse as the rest of the crew learn that both Iscandar and Gamilus are twin planets situated at the same star system. Meanwhile, despite knowing that Yuki is not Yurisha, Dessler takes advantage of their resemblance to rally his fellow Gamilas in an attempt to take over Iscandar. As the Yamato is about to reach their destination, the ship is targeted by an unknown enemy weapon.

After being almost destroyed by Dessler's own Wave Motion Cannon, Okita orders the Yamato to launch an offensive at the Gamilas capital and Dessler escapes to his space fortress, the "Second Baleras" in a ship with Yuki on board. Dessler then drops a part of the fortress on the capital in an attempt to vanquish the Yamato while sacrificing his own people and while the rest of the crew engage it, Kodai departs to rescue Yuki by himself.

With Dessler apparently dead and the Gamilas ceasing their hostilities, the Yamato at last reaches Iscandar, but Queen Starsha is in doubt about providing the assist she promised upon seeing that the Earthlings used the technology she entrusted to them as a weapon of mass destruction. After coming with a decision, Starsha reveals to Kodai the ultimate fate of his brother as the Yamato prepares itself for the long journey back to Earth.

Carrying the device that can restore Earth's environment, the Yamato is on its way back to Earth when Dessler, who was presumed dead, appears for a final confrontation.

The Yamato is on the last legs of their journey through outer space. However, a heartbroken Kodai has little to celebrate as Yuki did not survive from the wounds she suffered in the last battle. While witnessing the suffering of his brother, Mamoru's spirit appears next to him to create a miracle.