The year is New Era 2185 and the galaxy has experienced four years of uneasy peace. In the wake of the destruction that the later months of the galactic civil war brought, people have begun to rebuild their lives. The Federation, forged by members of the old Alliance Senate and other important political figures, has become the galaxy's governing body. The ashes of the Great War would also see a resurgence of large corporations and technological development firms that once flourished.

Among the heroes of the Great War was Alpha Squadron, led by Myles Warren and later Antes Eslos. Despite their heroic actions which led to the destruction of the demon weapon only known as Nova Fortress, the squadron was officially disbanded, a victim of bureaucratic litigation. Unofficially, pilots from Alpha Squadronwere responsible for training the next generation of fighter pilots at Hammerhead Alley—Aloyo.

Neo Pegasus, led by another hero from the Great War, Spade Jaqsun, was relegated to heavy sanctions by the Federation with the signing of the Treaty of Bartholomew. Relocated to an isolated star system and allowed to start anew, Neo Pegasus was forced to absolve their defense force and cease searching for any advancements in research and development, in turnleaving it a shadow of its former self.

The so-called peace, however,would not last long.

A race of technologically advanced, extragalactic aliens, led by the son of a great hero from the past, has declared war on the galaxy. It is now up to the battle tested heroes of the Great War to save the galaxy once again. And at the heart of the conflict are the ones with whom the galaxy's last hope for survival rests…

…Alpha Squadron.