The alien JAM have been at war with humanity for over thirty years...or have they? Rei Fukai of the FAF's Special Air Force and his intelligent plane Yukikaze have seen endless battles, but after declaring "Humans are unnecessary now," and forcibly ejecting Fukai, Yukikaze is on her own. Is the target of the JAM's hostility really Earth's machines? And have the artificial intelligences of Earth been acting in concert with the JAM to manipulate Yukikaze? As Rei tries to ascertain the truth behind the intentions of both sides, he realizes that his own humanity may be at risk, and that the JAM are about to make themselves known to the world at large.