During an official visit by Senator Armstrong (Chris McDonald), his assistant Chloe (Elyse Levesque), and Eli Wallace (David Blue), a recently recruited gaming genius, to a secret off-world military base, a surprise - and ferocious - attack leaves Colonel Everett Young (Louis Ferreira) with no choice but to retreat. He orders an evacuation to Earth. A last-minute maneuver by scientist Dr. Nicholas Rush (Robert Carlyle), however, thrusts the escapees headlong into his experiment, which transports everyone to deep space.
The survivors arrive on an uninhabited ship floating billions of light years away from Earth. Panic spreads throughout the group and Col. Young, who was severely injured during the escape, transfers command to Lt. Matthew Scott (Brian J. Smith), before lapsing into unconsciousness. Teams led by Dr. Rush and Sgt. Greer (Jamil Walker Smith) try to make sense of the situation, while Lt. Tamara Johansen (Alaina Huffman), a medic who was days away from leaving the program, is thrust into the role of chief medical officer.
After secretly contacting the Home World Command using communications stones - a device which allows the swapping of consciousness between bodies across vast distances - Dr. Rush claims that he has been placed in charge by General O'Neill (Richard Dean Anderson) and there is no hope of returning to Earth. When the ship's air supply systems begin to fail, his theories are challenged by Eli. As the crisis deepens, divisions emerge between those who want to attempt a return to Earth, including human resources executive Camille Wray (Ming-Na), and those who want to remain aboard the Destiny.