In A.D. 2040, the story unfolds on Planet Eden, humanity's first emigration planet more than a dozen light years away from Earth. The U.N. Spacy is preparing to decide on the successor of the next Variable Fighter through Project Super Nova. Isamu Dyson, an outstanding pilot assigned to the Variable Fighter YF-19, is reunited with his childhood friend Guld Goa Bowman, who is also the test pilot for YF-21, the competing Fighter. At the same time, Myung Fang Lone, the producer of Sharon Apple, a popular Virtual Singer, who also happens to be Isamu and Guld's childhood friend, arrives at Eden. The three, whose paths once diverged after a certain incident in the past, come together once again.

Entrusted with the latest Variable Fighters, Isamu and Guld confront each other with their own pent-up emotions while Myung watches the event unfold. Amid this conflict, Sharon causes a major stir in their relationship.

Isamu is sent to the medical pool after an injury, while Myung decides to leave for Earth. Meanwhile, the U.N. Government prepares to conclude the development of Ghost X-9, an unmanned Fighter with exceptional mobility.

Isamu takes YF-19 and heads to Earth in an attempt to stop Ghost X-9, while Guld chases him with YF-21. With Ghost X-9 set loose and the Macross in Isamu and Guld's way, what fate awaits the three?