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Humanoid aliens known as the Buff Clan discover the Earth colony planet Solo, where archeologists have found 3 large armored trucks from the 'Sixth Civilization' a long extinct alien civilization. Karala Ajiba, daughter of the Buff Clan military commander heads down to Solo along with her assistant Mayaya and is pursued by her colleagues Gije Zaral and Damido Pechi. A panicked Buff Clan soldier attacks one of the Solo excavation sites, triggering an interstellar war. Seeking cover, some of the colonists including Cosmo Yuki, Kasha Imhof, Bes Jordan and Sheryl Formosa board the armored trucks, which combine to form the god-like mecha, Ideon, which fights off the enemy.

The Ideon's 3 vessels revert to their normal forms after the battle is over and are equipped with powerful weapons under the direction of Bes. Bes later runs into Karala in the woods, mistaking her for a colonist. Gije leads an attack on Solo to rescue Karala, and totally destroys Solo's capital, New Lopia. Fleeing from the attack, a group of children including a baby, Piper Lou, board the Ideon, which finds the strength to fight off the Buff Clan once again. Sheryl meanwhile heads to the second excavation site, where a giant spaceship has been discovered.

Karala is reunited with Mayaya aboard the Solo Ship. Gije and Damido request help from their commander, Abadede, and launch yet another attack on Solo in order to rescue Karala. Bes discovers that Karala and Mayaya are actually Buff Clan aliens. During the ensuing battle with the Buff Clan, the Solo Ship rises from out of the ground.

As the colonists prepare to flee the planet onboard the Solo Ship, Cosmo and the others continue testing the Ideon's capabilities. Different factions within the Buff Clan argue about their next course of action, and another group attacks the colonists. Karala continues to explore to discover more about the legend of the Ide, but the ship still holds some surprises for both the Buff Clan and the colonists.

The Buff Clan attack again, this time as a distraction to allow Gije to sneak aboard the Solo Ship on a rescue mission. He finds Karala and Mayaya, but the three are quickly recaptured. The colonists interrogate the Buff Clan members, and Karala explains the legend of Ide.

The colonists decide to attempt to negotiate a ceasefire with the Buff Clan. In order to signal their intentions, Cosmo raises a white flag above the Solo Ship, not knowing that the white flag means something different for the Buff Clan than for humans. Reading the signal as a challenge, the Buff Clan attack.

The Buff Clan give up on rescuing Karala and lauch a full-scale assault on the colonists. The Solo Ship flees to subspace, but they're closely pursued by the Buff Clan. Gije faces off against the Ideon piloting the Buff Clan's latest weapon, the Heavy Mobile Mecha Giran Dau.

Still seeking to escape their pursuers, the Solo Ship exits subspace at an unknown location and the colonists find themselves on a planet full of dinosaurs. Two of the young children decide to explore, but they run afoul of the local wildlife. Cosmo and the others take the parts of the Ideon out to look for them, but before they can get the children back to the ship they encounter Gije, who demands an honorable duel.

The crew of the Solo Ship decide to abandon it and make a deal with Marshall Franklin such that they can take refuge and the Solo Ship will be destroyed. However shortly after departing, Franklin betrays them and sends his troops to recover the Solo Ship and disarm the bombs on board. As the Solo Ship's crew rushes back to it, a Buff Clan fleet also arrives and a three way battle ensues, in which Franklin is killed. The Solo Ship's crew fails to disarms the bombs in time, but the Ide creates a protective barrier that prevents it from being destroyed.

The Solo Ship returns to the planet Ajian seeking refuge from the Buff Clan. Bes makes a deal with Ajian's leader, Commodore, such that the civilians of the Solo Ship will be allowed to remain on Ajian. Commodore conspires with a Buff Clan officer and instead ends up taking all of the civilians hostage, killing Sheryl's sister, Lin. Bes, Gije and the others rush back to save them and Sheryl ends up killing Commodore. Doba, unsatisfied with the performance of his officers, personally starts heading out to take on the Solo Ship and Ideon.

The Solo Ship lands on the planet Steckin Star in order to rest before yet another battle. Harulu sends her forces there and a battle ensues. During the fighting Gije is killed and the Ideon goes berserk, slicing the entire planet in half with the Ideon swords.

Karala and Joliver are transported to the Buff Clan flagship, the Bairal Jin. There, Karala encounters her father Doba, and reveals to him that she is pregnant with Bes's child. The Solo Ship and Ideon rush to the Bairal Jin to rescue Karala and Joliver. Although their shuttle is destroyed in the battle, Karala and Joliver are protected by the Ide and make it out alive. As the Solo Ship escapes, Doba demands his army to follow them. With the meeting between Doba and Karala ending up as a failure to reconcile the differences between humanity and the Buff Clan, the Ide wipes out both races.