An attack on a secret off-world base by a rebel organization has stranded the remaining survivors on an Ancient ship "Destiny", a large unmanned ship launched millions of years ago.
At the far end of the universe, Colonel Everett Young and Dr. Nicolas Rush now lead the new "Destiny" crew on a journey to discovering new worlds as well as encountering new alien creatures, in hope of finding a way back home.
Morals are tested and tensions rise when Colonel Young's leadership is questioned all while Dr. Rush sacrifices the safety of the crew to pursue his own scientific ambitions.
Along the way, they make new enemies and clash with old familiar ones, as they uncover the mystery behind Destiny's true purpose.