The game begins 32 years after the Great War. You are a pilot in the Galactic Terran-Vasudan Alliance (GTVA), a single entity formed to cement the alliance between the Terran and Vasudan races after loss of communication with Earth. However, opposition still exists to this union, and a faction of Terrans led by Admiral Bosch formed the Neo-Terran Front (NTF) and has rebelled, taking over several star systems. The player's early missions are to quell these rebellions and bring in Admiral Bosch. Eventually the another alien species is encountered.
Thirty-two years have passed since the Lucifer was destroyed. Its reactors were breached causing it go nova as it exited the SOL jump node. Since then the Earth has been cutoff from the rest of the galaxy.
A group of rebels, the Neo Terran Front (NTF), have been putting a huge strain on the Terran-Vasudan relations and the new Galactic Terran-Vasudan Alliance (GTVA). Due to a discovery made by the NTF, an ancient device created by the "Ancients," a portal has been opened leading directly into Shivan space. The Shivans from "The Great War" are back and they are pissed off. You, a member of the human "Lost Generation", will have to answer the call to war.