The player takes on the role of Mobius 1, an elite fighter pilot serving in the Independent States Allied Forces' (ISAF) air arm, fighting against the Eruseans who have occupied almost all of the Usea continent after an apocalyptic event in 1999. A massive asteroid, codenamed Ulysses 1994 XF-04, struck Usea, killing 500,000 people and turning many into refugees. Erusea used this as an opportunity to occupy the continent after a prolonged military buildup. They achieve military supremacy via the superweapon Stonehenge, a megastructure battery of railguns that were originally designed to destroy asteroids but have been found to be effective against airplanes as well. This allows Erusea to dominate much of the airspace over the continent giving their military a powerful strategic advantage. Consequently, ISAF has been pushed back to the eastern coast of Usea.
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\nBetween missions, a story is told through twelve interlude flashbacks, later revealed to be a long letter to Mobius 1 about the war and living inside the occupation. The letter is written by an unnamed man, whose parents were killed when an ISAF fighter jet crashed into their house in San Salvacion when he was a child. This fighter jet was shot down by Yellow 13, the Eruseans' top fighter pilot, and a member of the Elite Aquila Squadron, well known as Yellow Squadron. Following his parents' death the boy is taken in by his uncle, a taxi driver who lives in the city above a tavern frequented by Erusean soldiers. While in the tavern, the boy befriends Yellow 13 after meeting him and the other Yellow Squadron members. He also learns that the owner of the bar is a member of the local resistance against Erusea and becomes a "spy" for them due to his friendship with Yellow 13.
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\nAs the war progresses, Mobius 1's contributions begin to turn the tide as the Allies begin retaking Usea. The situation in San Salvacion becomes more desperate as the ISAF forces advance closer. The boy recalls one event where the bar owner's daughter plants a bomb on the airfield, which severely damages Yellow 4's plane and greatly angers Yellow 13, since Yellow 4 is his closest friend (and possible love interest). ISAF then attacks Stonehenge itself and Mobius 1 manages to destroy it. Yellow Squadron arrives too late to affect the battle, but nonetheless engage Mobius 1 only to have Yellow 4 shot down and killed. Yellow 13 is also eventually shot down by Mobius 1 in a later battle. Following the capture of the Erusean capital Farbanti, as well as the general surrender of all Erusean military forces, a group of young rogue Erusean officers activate another superweapon, Megalith, which is a missile launch facility capable of shooting down the asteroids from orbit to crash them into any location on the planet. Mobius 1 is given his own squadron of the best ISAF pilots available and they assault Megalith, destroying it and ending the war once and for all.