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.

A.D. 2089 - 80 years have passed since Space War I changed the lives of both human and Zentraedi races. Both races are at peace on Earth when a new alien race called the "Marduk" appear within the Solar System. While covering the first battle between the U.N. Spacy and the Marduk fleet, SNN rookie reporter Hibiki Kanzaki discovers Ishtar, an "Emulator" that enhances the Marduk's combat abilities through singing. Hibiki brings Ishtar to Earth to teach her the values of life and culture. Together with ace Valkyrie pilot Silvie Gena, Hibiki and Ishtar must find a way to save Earth from total destruction at the hands of the Marduk leader Ingues.