In 2040 A.D. on the colonial planet Eden, the Ministry of Defense is testing and developing a transforming aircraft, a new advanced defense to counter alien threats. Isamu Dyson is an extrovert jet fighter maverick assigned as a new test pilot on project Super Nova. Competition heats up when he discovers that his old rival Guld is test pilot for the competing project. The arrival of Myung, a mututal ex-girlfriend, adds mor tension to the conflict.

Computer-generated mega-pop star Sharon Apple has packed in the masses again for another of her bestselling concerts. Amongst the fans are, Isamu Dyson, the maverick pilot, and Yang, who is about to pull off one of the biggest computer hacking stunts ever in front of millions. When Isamu returns to the New Edwards Test Center he is up against his old rival Guld for air supremacy as well as fighting for the affections of Myung, the discontented producer of Sharon Apple. A computer transmitted message alarms the pilots that Myung is in danger and both rush to her resuce. Guld emerges a hero and Isamu is jealous. Sparks fly and rivalry turns violent as they meet in ariel combat.

A firestorm of emotion ignites when the dangerous rivalry between hotshot renegade Isamu Dyson and ice-cool Zentradei helf-breed Guld Bowman reaches the boiling point amid the pressure of the Super Nova test program. Former singer Myung Lone, now the manager of the computer-generated virtual idol Sharon Apple, is torn between her feelings for the two men as her memories of days gone by on planet Eden are shattered by harsh reality. After an investigation into the so-called 'accident' that left Dyson hospitalized, the UN Government in charge of the test program unveils its hidden agenda and cancels both Dyson and Bowman's experimental star fighters in favor of a new artificially intelligent aircraft. Myung leaves them behind, heading for Earth and an uncertain future, while Dyson, with the help of hacker genius Yang, hijacks the YF-19 fighter and heads after her. Only one other plane can catch him -- the rival YF-21. Bowman climbs aboard and the chase is on... Meanwhile on Earth, on the eve of her greatest concert, the computerized Sharon Apple has become self-aware for the very first time ... and the consequences can be murder...

Angered by the news that the Stealth Valkyrie trials have been abruptly stopped, Isamu and Yang head toward Earth to get even with the pilot-less Valkyrie, "Ghost X-9." Guld, also hearing the same news goes after them for a final battle. The two fighters clash amidst interceptor missiles being fired from Earth. During this fight to the death, Guld recalls a fateful event that had been sealed in his memory. Meanwhile, in Macross City, Sharon Apple absorbs Myung's thoughts and twists them in a terrifying fashion. She now has full control over the city as well as the minds of its citizens. Sharon sends the "Ghost X-9" after Isamu and Guld.