In 2199, five years after the Gamilons began an invasion of Earth, the planet has been ravaged by the aliens' bombs. The remnants of humanity have fled underground to escape the irradiated surface. One day, former pilot Susumu Kodai discovers a capsule sent from the planet Iscandar that tells of a device that can remove the radiation from the Earth's surface. The Earth Defense Force rebuilds the battleship Yamato with a new type of propulsion system to make the 148,000 light year trip to Iscandar in hopes of saving the Earth. Within one year, the radiation will drive the rest of humanity to extinction.

2199 AD. Yamato tried to leave behind the Large Magellanic Cloud galaxy, after receiving a "Cosmo Reverse System" at its destination, Iscandar. However, suddenly, it encounters a mysterious group at the edge of the Large Magellanic Cloud. The crew finds out that the group is called the "Gatlantis," and that its leader is the Gutaba expeditionary force commander who calls himself "Goran Dagaamu of Thunder." The commander demands that Yamato be handed over to him. Yamato, wanting to hurry to Earth, escapes the fray. However, Yamato is attacked by a devastating beam weapon called the "Flame Direct Attack Cannon" that can transcend space.

When vile aliens known as the Gamilons wreak nuclear havoc on Earth, a group of survivors refit the Japanese battleship Yamato for intergalactic travel and set off on a mission to retrieve a neutralizer that will eradicate the radiation from Earth's atmosphere.

The Galman Empire is destroyed but the planet Galmania is not, by a chance collision of galaxies. The Bolar Federation worlds including Planet Bolar are destroyed. The Yamato, back under the command of Captain Okita, encounters the planet Denguil too late to save its humanoid civilization from being flooded by the water planet Aquarius. The surviving Denguil, a warrior race who believe only the strong should survive, plan to use Aquarius to flood Earth and destroy humanity, in order to create a new home for their race.

In the year 2220 A.D., the Earth Federation launches a plan to evacuate Earth when discovering that a travelling 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.

Compilation film of "Space Battleship Yamato 2199" TV series. The year is 2199. The human race has been crushed in their war with the Gamilos, driven into underground cities by the invader's assault. Scientists estimate they have only a year left. The young officers Susumu Kodai and Daisuke Shima receive a mysterious capsule from a ship that made an emergency landing on Mars and return with it to Earth. It contains humanity's last hope: the planet Iscandar on the other side of the Magellan Galaxy has the technology to defeat the Gamilos and restore the planet. The space battleship Yamato is entrusted with this task, but they have only one year before humanity ends.

Time to ease up ... not! Although the Yamato's crew has witnessed the end of the long, hard-fought Comet Empire War, a peaceful future will have to wait. While Dessler gathers together the shattered remnants of his Gamilus Empire, new forces are at work in the universe that could augur in another conflict. Seems the Black Star Empire has invaded Dessler's homeworld and is decimating it, all the while gathering power for its war machine.

The anime's story is set in the year 2202, three years after the Yamato's return from the planet Iscandar. The people of Earth restored their planet with the Cosmo Reverse System, and they signed a peace treaty with Garmillas. In addition to reconstruction, Earth developed a new defense fleet that includes the state-of-the-art battleship Andromeda. The Earth goes down a path of military expansion, despite Starsha Iscandar's wishes. The Yamato helps accomplish this so-called peace, but it comes at the price of many invaluable sacrifices. The goddess Teresa, who prays for tranquility in space, calls the Yamato to a new voyage. The threat of Gatlantis is sweeping over the universe and approaching Earth.

Theatrical release of episodes 15-18 of Space Battleship Yamato 2199.

Theatrical release of episodes 7-10 of Space Battleship Yamato 2199. Deals with contact with the Galamis (Gamilon) enemy and offers an original story that delves into areas that the first Space Battleship Yamato anime did not explore.

Theatrical release of episodes 11-14 of Space Battleship Yamato 2199.

Theatrical release of episodes 23-26 of Space Battleship Yamato 2199.

Theatrical release of episodes 19-22 of Space Battleship Yamato 2199.

Second theatrical compilation of the Space Battleship Yamato 2199 series, featuring episodes 3-6.

Compilation of episodes 1-2 of the Space Battleship Yamato 2199 TV anime.

The Yamato and her crew face the onslaught of the Comet Empire, a civilization from the Andromeda Galaxy who seek to conquer Earth, led by Prince Zordar. They have harnessed a comet and is using its terrible power to unleash destruction upon its rivals and inferiors... which are in fact everyone. The Space Battleship Yamato heads back into action. But this time, it shall not return, and much of the Yamato crew have signed on for their last voyage.