It has been 33 years since an alien race, known as the JAM, emerged from a hyperspace passage over Antarctica with the sole purpose of invading Earth. Despite their unexpected initial assaults, a combined effort by humanity not only pushed the JAM force off of Earth but also moved the frontlines of the battle onto the JAM's homeworld of Fairy. Though out of sight and mind for the majority of Earth's inhabitants, the conflict still rages on Fairy, where the United Nations has established five bases and a powerful, technologically advanced military—including the Fairy Air Force (FAF).

Lieutenant Rei Fukai acts as a pilot for the FAF Special Air Force’s Boomerang reconnaissance squadron, flying a Super Sylph fighter jet with the personal name "Yukikaze." Soaring high above and observing the battles for air superiority, he is responsible for collecting and analyzing valuable intelligence on JAM methods. While his flying skills are unmatched, he also heavily relies on the highly advanced weaponry and near-sentient AI system of his aircraft.

Though despised by other members of the FAF for his antisocial and standoffish nature, Lt. Fukai continues to carry out his duties along with Yukikaze. However, during a particularly bloody battle, the appearance of an unresponsive and hostile aircraft catches the lieutenant off-guard—an aircraft which is of the same make and model as his own.