When the last space fleet of the UN forces fight against Gamilas forces near Pluto, a mysterious spaceship make a emergency landing on Mars.

The space battleship Yamato is the human built in secret. Yamato has to trip to the planet Iscandar, 168,000 light-years away from the Earth.

Yamato has engine trouble during the test of the warp drive system. When the crew are repairing it at Jupiter, Gamilas forces attack on Yamato.

There is a Gamilas meteorite-bombs launching base in Pluto. Earth is devastated by the bombs until now. Captain Okita decides to attack on the base.

Yamato Space Flying Corps keep looking for a enemy base in Pluto. During the confuse fight, Kodai finds out something.

Yamato going to pass the Heliopause. The crew are allowed to contact each of their family, have endless sorrow of parting.

In Gamilas capital, Dethler will show the state that Gamilas forces attack and sink Yamato by his strategy, because wants to show off his power to cabinet ministers.

During AU09 (a.k.a. Analyzer) analyzes a Gamilas android-soldier that Yamato's crew captured, friendship has begin to grow between them. Are there the heart in the machines?

Yamato falls into the dimension-fault where wrecked many spaceships, such as the graveyard of the universe.

Yamato crew's opinions are opposed about Melda who survived a pilot of Gamilas forces.

Which started the war, UN or Gamilas? The question and the truth makes a gap between Kodai and Shima. Meanwhile, Dethler orders Domel to subjugate Yamato.

While the invisible enemy attack on Yamato, Cap.Okita collapse from his illness.

When Kodai and Yuki came back from reconnaissance, it seems that not a soul was to be seen in Yamato.

The crew feel distressed by persistently attack of Domel. Finally, some crew have raise doubt about Yamato's mission.

The planet named Bemera-4 where Yamato stopped for supply is Earth-like world. Niimi and Itou lead a mutiny to abandon Yamato's mission, and they want to let people emigrate from Earth to Bemera-4.

Kodai brings a information back from the relics of Bemera-4. It seems that Yamato will be enabled to jump tens of thousands light-year by the hyperspace gate network in the relics.

Shinohara uses hyperspace gate network, and goes on a scouting flight to Balan. Unfortunately, there are ten thousand of the battleships of Gamilas forces for naval review.

Dethler orders Domel to subjugate Yamato again. However, Domel was given that child soldiers, old soldiers, and four aircraft carriers.

Yamato, the Carrier Strike Group under the command of Domel, the two forces confronting each other in the Rainbow Star Cluster.

The prison planet 17 is one of Gamilas's concentration camp planet for political dissidents and POW. In this camp where a prisoner is abused routinely, but the supervisor will come from Gamilas.

Cap.Okita found the position of Iscandar and Gamilas, and orders the crew to jump toward Iscandar.

Just after warp out, Yamato was attacked by high energy beam.

A few Yamato crew meet with Queen of Iscandar, Starsha. She tells totally unexpected for them.

Yamato leaves Iscandar for home. They go to Balan to use hyperspace gate network, but the remnants of Gamilas forces ambush there.

Yamato come back into the Solar System. And a miracle will happen to crew.