In Advent Rising, a common legend pervades the galaxy - that of a powerful, ancient race that will one day unite the universe. Millions of cultures from vastly distant worlds revere and hallow these mythological beings known as humans. One race, the Seekers, know humans actually exist and are threatened by their potential power. Under the guise of benevolent explorers, the Seekers travel throughout the galaxy in a desperate attempt to eradicate any human society they unearth.

Players assume the role of Gideon Wyeth, a remnant of the last human outpost, on the brink of discovering the incredible powers that lay dormant within him. It is these powers the Seekers are so desperate to suppress.