Unbeknownst to the general population, 33 years ago, an alien force, the JAM, opened an interdimensional 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. However, the recent infiltration of human disguised-JAM agents has begun to blur the lines between friend and foe. As the SAF's own fighters begin to turn against their own forces, the Final Battle for the skies of Fairy and control of "the Passageway" to Earth will rest in the hands of Rei, and the only thing he can trust: the Yukikaze.