Lieutenant Kei Katsuragi, a fighter pilot, receives a mission to protect a new untested bomb, the Space/Time oscillation bomb. During the mission the bomb goes off, and it produces a catastrophe.

Kei learns that the Emaan are the natural inhabitants of this world and that they are at war with the Terram, another race. He also learns that he cannot return home, because this world is surrounded by a dimensional barrier that can't be destroyed.

Mimsy, one of the Emaans, finds Kei and brings him back to the others. He discovers that the Emaan fighter planes have an anti gravity control system which makes them easier to pilot.

Kei and Mome, a robot girl, decide to look around while the others are rebuilding his Bronco. They arrive in a Terram villaige, where Kai sees a man driving a jeep. The man says he got it from the Emaan, who were the ones who fixed it.

The Emaan are welcomed by the villagers after they offer them some free goods. That night, at dinner, Jaby suggests that they rename the modified Bronco Orguss, after their god of war.

Jaby convinces Shaya to stop the Glomar, their caravan, to search for a valley where he believes they will find grapes, which is his favorite food. They arrive in the valley, where they find some huge grapes and decide to stop to harvest them and take them aboard the Glomar.

Mome, the robot girl, has become infatuated with Kei and always wants to be near him. Kei however doesn't really care about her.

Kei and the others discuss possible escape routes for eluding the Terram. The best one seems to be fleeing over mainland France.

The Glomar is hovering above a battlefield, where they meet some survivors, rebels led by Jann who asks the Emaan to help them overthrow the aristocracy. The Emaan already made a contact with Ann months ago, lending her a powerful weapon called the Hasai Cannon. They didn't expect Ann will use it to suppress the peasants, so they agree to help the rebels overthrow Ann and get the weapon back.

After a game of tennis, Kei and Sray continue to argue over Mimsy, and Kei tells Sray that if Mimsy is his woman, he should try to defend her.

The Emaan agree that if Kei would die, all of their problems would be over.

The Terram supreme commander gives Athena, one of their best pilots, their newest ship, the Nikick. Her mission is to bring Kei to them, alive.

In order to increase the jamming field of the Glomar, the Emaan decide to send someone out with another jamming device. Shaya mentions that the person who will do it will most likely be found and killed by the Terram. Sray decides to volunteer for this mission.

The Terram supreme commander gives new orders to his army: Kei, the Tokuiten, as they call him, has to be killed. Otherwise, his actions could ruin their secret project, the D-system.

Olson confronts Kei, explaining to him what the Tokuiten really is, and tells him that he should come with him back to the Terram so that they can undo the mess the world is in.

The Galmor finally arrives at the Emaan homeland. There, Kei is captured by members of the Toobu clan who wish to brainwash him. Shaya leaves on a mission to save him.

Sray returns to the Galmor to find Mimsy ill. She is ending her period of fertility, and soon she will no longer be able to have children.

Shaya meets with her sister, Manisha, to discuss about the Tokuiten. Shaya refuses to give Kei to the Toobu.

During their fight, Kei and Athena are sucked through a dimensional warp and find themselves in World War 2 era. There, they are forced to take refuge inside a cave, where they get a chance to know each other a little better.

Olson returns to the Galmor to try and convince Kei to come with him to the Terram, in order to repair the world. Kei refuses, but learns more about Athena.

Athena returns, and fights Kei. Olson stops the fight, and tells Athena the truth about her relationship with Kei.

Kei must decide now whether to remain with the Emaan or return to the Terram.

The Terram finally complete their D-system, which will allow them to travel through space and time. Using it, a critical time can be found and a bomb planted which will alter history, causing the world to mend. However, the device does have its dangers; misuse of the device could destroy space and time completely.

The Mu leader reveals his plan: to create a world ruled by the superior machines. But, to do so they must destroy both the Terram and the Emaan.

The Galmor is under attack by the Terram army. Olson is lured into a canyon by Robert. There, Olson tries to convince Robert to desert the Terram army and help the Emaan, like he did.

The Terram are under attack by the Mu, and Athena is put in charge of defending their precious D-system. Seeing no alternative, she is ordered to press the auto-destruct button of the D-system.

Athena attacks the Emaan once again. Olson and Kei try to convince her how important their mission is.

The Terram show Manisha and Shaya footage of a Mu assembly, in which their leader proclaims that they will be victorious and conquer all of space and time.

Both Mome and Tai become depressed now that the Mu is their common enemy.

The Mu attack an Emaan city, and both the Terram and the Emaan mobilize their forces to combat the enemy.