On the planet Solo in the Andromeda Galaxy, a group of archaeologists have come across the mysterious remains of the Ideon—three large armored tanks with the ability to combine into a godlike mecha.
Cosmo Yuki, the afro-wearing protagonist of the series, and his friends Kasha Imhof and Deck Afta climb aboard the three tanks, which activate on their own, and, when they initially combine to form the Ideon, fend off the first assault, repelling Gije's men.
Gije and his partner Damido, meeting up with the leader of their expedition, Abadidi Gurimade, soon launch more attacks on the planet Solo in an attempt to capture the Ideon (which they refer to as the 'Giant God').
The survivors flee inside the Solo Ship and Karala and Mayaya, who are mistaken by Bes as a colonist, are let onboard as well.
Other civilians who quickly get onboard the Solo Ship include Sheryl Formosa, a linguist studying the civilization on Solo; Sheryl's sister, Lin; Banda Lotta; three children: Piper Lou, Ashura Nobaku, and Fard Maraka; mechanic Joliver Ira, pilot Hatari Naburu; and Moera Fatima.
The Buff Clan force chases the Solo Ship to the planet Crystal Star, where Abadidi heads out himself in a Dogg Mack.
Arriving on the planet Ruins Star, Karala tries to make peace with her sister, but is humiliated by Harulu's underlings.
Things get even worse for her when Banda Lotta, upset by all the harm the Buff Clan has caused, tries to kill her, but folds under pressure.
The Solo Ship arrives at an Earth base where Cosmo meets Camyula, a female officer who reminds him of his mother.
Gije heads back to the Buff Clan homeworld as the Solo Ship travels to the planet Flag Star.
Harulu flees in an escape capsule and meets up with Daram Zuba, a former lover and member of the Ome Foundation, which is plotting with Doba to overthrow the Buff Clan Emperor.
There, Cosmo meets Kitty Kitten, who desires for the Solo Ship to flee, since it will bring nothing but more heartbreak to their wartorn planet.
The Solo Ship returns to Ajian, whose inhabitants now despise them for what happened earlier and their military leader takes hostages, killing Lin before he is stopped.
The Solo Ship flees to the planet Steckin Star and Gije is killed when the Ideon is heavily damaged.
With repeated failure by his military leaders, Doba himself heads out on the Buff Clan flagship, the Bairal Jin.
Bes tells Hatari to pull back the Solo Ship and have the Ideon protect Karala and Joliver.
After Doba declares that he will hunt his daughter to the ends of the universe, the Solo Ship flees under pursuit of many Buff Clan troops.
Sheryl, drunken and mad over Lin and Gije's deaths and armed with the knowledge that the Ide desires to protect children, brings out Piper Lou onto the deck of the ship in order to strengthen the Ideon.
On the bridge of the Solo Ship, Karala reveals to everyone else that she's pregnant with Bes' child, who Cosmo and the others call a Messiah.
Kilarul and Tororof head back to Harulu, telling her that Karala and her unborn child are what manifest the Ide.
Harulu decides to both prevent the child's birth and stop the Ide's power from invoking by killing Karala.
Meanwhile, meteors strike Earth, its colony planets, and the Buff Clan's homeworld, killing everyone and reducing them to uninhabitable wastelands.
Doba, angry with the deaths of his daughters, has the Buff Clan military force continue to attack the Solo Ship as it approaches the Gando Rowa.
In the ensuing battle, Kasha is killed by shrapnel and Buff Clan soldiers make their way to the Solo Ship bridge.
The Ide is invoked as the Ideon and the Gando Rowa are destroyed by a resulting blast wiping out the entire universe.
As a result, they sold out quickly and it was not uncommon to see the second boxset alone command a price of over 80,000 yen used on such websites as Yahoo!