The human race has beaten an invasion by an alien race called the JAM back to its home planet Fairy. Fairy Air Force, the UN-mandated military organization tasked with neutralizing and eventually eliminating the alien threat, assigns and armed strategic reconnaissance aircraft codenamed "Yukikaze" and equipped with an AI to Lt. Rei Fukai of the subordinate Special Air Force with the intention to record data on JAM movements and battlefield tactics. One day, however, an encounter with the "Grey Sylph" (a JAM duplicate of the Yukikaze) lands him in hot water with his superiors. During another patrol, Fukai is captured by JAM clones wanting to study the plane. He kills one of his captors and escapes with the plane from an alien entity disguised as a FAF forward airbase but ends up being pursued and shot down by the "Grey Sylph". As the "Grey Sylph" attempts to finish off Fukai's aircraft, the Yukikaze AI hijacks an FRX-99, a prototype UCAV that was undergoing operational tests at that time, and uses it to destroy the "Grey Sylph". The AI uploads its files to the FRX-99, ejects Fukai, and obliterates Yukikaze's wreckage.