Twenty-five years after a mysterious being called 'The Avatar' averted war between Earth and the Crogs, Earth is invited to participate in "The Great Race of Oban", a competition held once every 10,000 years. Meanwhile, a young girl escapes from her boarding school on a journey to find the father she hasn't seen in 10 years...

The 'Earth Team' arrives on Alwas, site of the preliminaries and discovers that Eva, who calls herself 'Molly', has accompanied them. With no time to argue, the team competes in their first race, but disaster strikes when their star-racer explodes at the finish line. With their star pilot, Rick, out of commission and no replacements, is the Great Race already over for them?

With no lead pilot, the Earth Team desperately searches for a replacement, that is until Molly jumps into the pilot seat and enters the next race. Even though she wins, Don Wei, blinded by his own pride, accuses her of humiliating him, and announces his intentions to withdraw from the tournament.

Molly is attacked by Groor after winning their race, but thanks to some assistance from Prince Aikka, is able to make it to the next race. The race, it seems, is fixed to be in favor of hometown hero, Flint, but the tables turn and Molly wins. Later, Don Wei learns that Rick has now recovered.

Rick recovers from the accident and becomes the lead pilot again, but something is wrong. While racing against Ceres, his muscles seize up and he is unable to control his hands or see clearly. Molly notices this, and races to catch up to the Arrow 2 to help Rick pilot. After the race is over, Rick is told he can never race again.

Molly is now chosen to take Rick's place as the new driver. However, the team's racer is sabotaged by Paradice, a cat-like creature who views The Great Race of Ōban as nothing more than a game. After a quick repair, they race against each other, and Molly inadvertently learns about the ultimate prize from Paradice.

While Rick searches for answers about who sabotaged the team's first racer, Molly races in the preliminary semi-finals against a commanding officer in the Crog army. The experience later proves to be disastrous as the Crog not only beats them easily, but destroys their racer in the process.

Molly and Aikka agree to a cease fire for their match, but Don Wei and Jordan think it would be better to take Aikka out. The race goes well at first with Molly keeping Jordan locked inside his turret, but near the end of the race, Jordan finally shoots at Aikka. Angering by this 'betrayal', Aikka retaliates, totally disabling the Arrow. The Prince loses all respect for Molly and her kind, and Molly, Jordan, and Don's bond is further severed.

Unable to reach Molly, who has shut herself up in her room, Don Wei decides to have Rick personally train her. Meanwhile, Jordan confirms a long-standing rumor, and then they race a familiar opponent.

Molly races Rush in a contest of marksmanship, seeing who can destroy the most targets. Meanwhile, Don Wei reveals his past to Rick, finally shedding light on how he became what he is today and why he 'abandoned' Eva.

With the finals slowly approaching The Earth Team prepares for its next race against Spirit. Upon seeing his face, both Don and Molly are horrified at the revelation that this racer may be connected to the race that led to the death of Maya, Molly's mom and Don's wife, years ago. During the race, Molly's focus is terribly blinded by sheer hatred, until the truth is finally revealed on two fronts.

Stan and Koji desperately search for spare parts to rebuild the Arrow II before the next race. Molly contemplates her future should she win the Ultimate Prize. Elsewhere, Rick finally comes face-to-face with the "Timeless One".

It's do-or-die time for The Earth Team. To reach Ōban they must win their last race in a rematch against Toros. Piloting a rebuilt Arrow with a new, untested hyperdrive, Molly must summon all her courage to face the vile Crog and pull out a win...or risk losing everything.

Finally, the Earth Team has made it to Ōban, the site of the grand finals. Before proper introductions are made, the races immediately get underway. With new and old rivals to face, a new "points" rule, and no time to study the courses, things are bound to be interesting for Molly and Jordan, as the true race for the Ultimate Prize begins.

As the second race of the finals approaches, Molly and Jordan have caught the attention of Lord Furter, a self-described pirate. The crude little alien prides himself on winning, by eliminating his opponents before the start of each race, and the Earth Team is his next target.

Facing both internal and external conflicts, Molly races hard to win her team some points and it looks like she may actually pull it off. However, her hopes are short-lived when two dangerous sisters take it upon themselves to 'educate' the humans in true racing.

The finals continue as the Earth Team has finally begun to catch up in the rankings. They soon face a bug racer, whose quest for the Ultimate Prize may not be so different from Molly's. Meanwhile, Don Wei is still haunted at the possibility that Molly may very well be his long-forgotten daughter Eva, and how such a possibility could effect the purpose of why they're racing in the first place.

The next race takes place in Oban's center, where the stakes are high, as future planets exist around them. Will Molly be able to win, or is the drama involving Aikka's change toward her too much to bear? Will Jordan finally have the courage to ask Molly if she likes him?

Molly discovers a conspiracy by other racers to take Sul out of the competition, but struggles with how she should use this information: Stay quiet and take the opportunity to advance in the rankings, or inform Sul and give up any hope of catching the overall points leader. At the same time, Canaletto begins to set his own plans in motion.

With the end of the grand finals approaching, Don Wei confesses that he knows Molly's true identity, and finally reveals why he left her behind ten years earlier, but Molly is not ready to make amends just yet. During the next race, a vicious attack by another racer results in a terrifying crash that may finally spell the end of the Earth Team's pursuit of the Ultimate Prize.

After crashing and becoming stranded due to the attack of another racer, Molly and Jordan try to make their way across Ōban to catch up with the temple before the start of the next race. Along the way they encounter the beings that created Ōban, and learn a terrifying secret about the true nature of the Ultimate Prize; One that could rob Molly of any chance of bringing back her mother.

Nothing is clear to Eva anymore. Personally, she doesn't see why she would want to race anymore, since she is unable to revive her mother because of what the Ultimate Prize's nature reveals. However, she can't throw everything away, since a Crog victory would lead to Earth being obliterated. Eva must stop Kross from winning.

The final race has arrived and the stakes couldn't be higher. Kross, having learned the Ultimate Prize's true nature, goes on a rampage taking down all racers in his path. In the end, all that stands in his way is Molly. When the smoke clears and the race is concluded, a fateful decision by the victor unleashes an evil that should have never been set free.

Canaletto is free and determined to regain his lost power. The remaining racers join forces in order to stop the powerful being from achieving his goal. However, Canaletto will not go down so easily and unleashes his dark minions to destroy them. The fate of the galaxy hangs in the balance and one racer makes the ultimate sacrifice to ensure victory.

The Great Race comes to a surprising and powerful end. Old grudges and past wrongs are finally forgiven. Ōban is reborn as a new Avatar steps forward. And a young girl faces a new, brighter future with her father.