The player is cast as the commander of the U.N.S. Apollo, humankind's first interstellar vessel, dispatched at light speed to investigate the source of a signal broadcast at Earth from one hundred and fifty light years away. On reaching the source, the crew is told that, due to relativistic effects, Earth has by now been taken over by the religious Cantharan Order, and the signal was a ruse from the friendly Ishiman, who wished to maintain humanity as a free race; the Ishiman planned to find a new world for the crew of the Apollo. Although the advanced but peaceful Ishiman are unwilling to enter into direct war with the Cantharans, the Apollo's crew is able to persuade them to supply a limited amount of their technology in an attempt to free Earth. Upon undertaking their new mission, the ship is renamed the Ares.