Unbeknownst to the general population, 33 years ago, an alien force, the JAM, opened an inter-dimensional gate in Antarctica to invade the Earth. In response to this threat, the unified forces of Earth formed a military unit to combat these aliens, successfully pushing them back to the planet codenamed: Fairy. Even now, the war still rages on. Rei Fukai, a pilot of the elite FAF unit of the Special Air Force (SAF), flies the Yukikaze, an advanced fighter with a near sentient computer control system. The line between friend and foe starts to blur as the JAM initiate their infiltration of the FAF disguised as humans and the FAF begin their deployment of unmanned fighters. The final battle over the skies of Fairy will determine who controls "the Passageway" and the fate of mankind will rest in the hands of Rei and the only thing he can trust: the Yukikaze.
S01:E01 - Operation 1
Over thirty years have passed since mankind's first contact with the mysterious alien force "JAM." As a member of the Special Air Force (SAF) stationed on Fairy Air Force Base, Rei Fukai's mission is to conduct reconnaissance as the pilot of his beloved Super Sylph, Yukikaze, and return to base, even if it means abandoning allies in distress. Jaded by these inhumane missions, Rei trusts only Yukikaze. One day, Yukikaze is attacked by an unidentified aircraft, but manages to shoot it down. But was it really JAM? Upon returning to flight missions after an administrative hearing, Rei is once more attacked by an unknown aircraft. The next thing he knows, he was awakened in a room within one of the Tactical Air Bases where Rei receives medical attention for his wounds. He only later learns that everything was part of a trap set by JAM. Rei narrowly escapes aboard the Yukikaze, but is attacked again and his cherished craft is destroyed.
S01:E02 - Operation 2
Rei lies comatose, wounded in combat, while Bukhar continues to conduct tests on FRX-00, an improved version of the unmanned fighter FRX-99 Rafe in anticipation of Rei's eventual reinstatement. But within the FAF, the System Corps had taken the initiative in pushing forward the development of unmanned aircraft. With their program already underway, Bukhar, adamant in his commitment to manned units, was left to stand in opposition to the System Corp's Colonel Gunow. It was under these circumstances that FRX-00, after saving an advanced FAND II from a JAM attack, suddenly recognized the TAB-15 as a hostile target and began to attack. At that moment, as if called back to consciousness, Rei awakens. Was the attack on TAB-15 the result of a malfunction? Or was it something more sinister…?
S01:E03 - Operation 3
Something happens aboard Banshee IV, a mammoth flying aircraft carrier circling plane Fairy at a broad orbit, and its proximal combat system suddenly goes berserk, shooting down a friendly aircraft as it tries to land. But what is the cause? Rei is sent to infiltrate Banshee IV together with Captain John of the Systems Corps, one of the engineers who designed Mave's avionics. As a child, Tom underwent a plutonium-powered artificial heart transplant that greatly affected his self-identity. Through their investigation, Rei grows to know and empathize with Tom. As their search deepens, Rei's suspicion that the Banshee is contaminated by JAM grows stronger until, ultimately, the two are struck with an even more horrific reality.
S01:E04 - Operation 4
Mave has been outfitted with the new "Super Phoenix Mk XI" engine, and Rei and Bukhar are ordered backed to Earth to conduct a combustion test in its atmosphere. Mave leaves planet Fairy and plunges into the hyperspace "Passageway" heading for Antarctica – with three JAMs hot on their tail. A dogfight ensues over the waters of Antarctica where the Japanese Navy Carrier Admiral 56 is deployed. On board the carrier is Lynn Jackson, a woman who has long watched the FAF wage battle with the keen eyes of a journalist. After the clash with JAM, Rei lands on the Admiral 56 and meets Lynn in person.
S01:E05 - Operation 5
FAF's Brigadier General Cooley, Major Bukhar, Command-in-Chief Laitume and the System Corp's chief commission Linneberg sit on the grass by the taxiway, speaking over tea. Their tense discussion is interrupted, however, with word that Colonel Ansel Rombert of the Information Analytical Center has raised a revolt – part of an all-out attack launched by JAM, But in truth, it was a diversionary measure used by Cooley and the others who had anticipated the attack to camouflauge the FAF's full retreat from Fairy. Under Rei's command, Mave lifts off. The underground city in the cavity beneath Fairy Base goes up in blazes at the hands of the rebels. Meanwhile, the FAF puts their withdrawal plan centered around the Banshee III into action. But up ahead, a JAM armada awaits…