A.D. 2040—Thirty years have passed since the battle between the Earth and Zentraedi forces changed the lives of both races. On planet Eden, a top-secret project known as "Supernova" is being held to determine U.N. Spacy's next-generation variable fighter. Competing to win the funding are Shinsei Industries' YF-19 and General Galaxy's YF-21. Piloting the YF-21 is Guld Goa Bowman, a half-human, half-Zentraedi. Shinsei receives its new test pilot in the form of the unruly fighter pilot Isamu Dyson, who was once a friend of Guld. Meanwhile, as Isamu and Guld furiously battle to see which of their fighters is superior, a Virturoid Idol named Sharon Apple is to perform her debut concert on Eden. In charge of Sharon is producer Myung Fang Lone, another former friend of Isamu and Guld. When the three meet each other, old disputes spark from a troubled past. Little do they know that their past incidents—along with the Supernova Project and Sharon Apple—will somehow bring them together.

The year is 2040 and the galaxy is flourishing with several colonies and advanced technology. AI is near perfection and the current top idol is the near-completed Virturoid Idol Sharon Apple. All that is missing are her actual feelings, which instead are supplied by Myung Fang Lone. Sharon's debut concert is on planet Eden, where at the same time, fighter pilots Isamu Dyson and Guld Bowman battle over air superiority for the "Supernova Project." Isamu, Guld and Myung were once childhood friends, but after an accident seven years ago, they went their own separate ways. With Myung back in the picture, the old disputes are once again awakened. And when an unstable and illegal AI technique is installed in Sharon, the situation is worsened.

Koji Nanjo, a young rock star, falls in love with soccer player Takuto Izumi. Koji eventually learns that Izumi's mother killed his father out of severe and intense love. Izumi took all the guilt for his father's murder and refuses to go pro because of fear that his past will be discovered by the media. Izumi detests Koji's company and encouragement and severely dislikes the attention from the press, but Koji cannot stay away for he soon realizes that his love for Izumi is very similar to the love that Izumi's mother felt for his father.

Shin Kazama, tricked and forced into flying for the remote country of Aslan, can only escape the hell of war by earning money for shooting down enemy planes or die trying. Through the course of the series, Shin must deal with the consequences of killing and friends dying around him as tries to keep his mind on freeing himself from this nightmare.