A.D. 2040 - Thirty years have passed since the battle between the Earth and Zentraedi forces changed the lives of both races. Since then, both humans and Zentraedi have colonized other planets in the galaxy.

On planet Eden, a top-secret project known as "Supernova" is being held to determine the replacement of U.N. Spacy's aging VF-11B Thunderbolt 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.