A snafu with the communications stones lands Col. Young's consciousness in an unknown being, resulting in a standoff between the Destiny and an alien vessel and the abduction of Chloe.

Dr. Nicholas Rush and Chloe suffer nightmares following their ordeal on the alien vessel, and Rush suspects that a tracking device may have been placed on the ship's hull. Later, a splinter group on Destiny executes a coup with life-threatening consequences.

Now firmly in control again, Col. Young and the other military personnel try to find a way to live with the civilians who tried to take control of the ship. When the Destiny prematurely drops out of FTL due to a computer glitch, they find both a sun and an Earth-like planet that should not be there. Rush concludes that the entire system was created by an alien race that is far beyond their imaginations. With the ship malfunctioning and a month's worth of repairs before it can jump again, several of the military and civilians decide to spend time on the planet. Hard feelings from the mutiny persist and it's an opportunity for everyone to mend fences. When the time comes to return to the Destiny, several of them decide they want to stay on the planet. Young is prepared to let them stay, but he imposes severe conditions.

Lt. Tamara Johansen tries to track down what is causing the crew to hallucinate.

Desperate for food and water, Rush directs the ship to a planet that has been locked out of Destiny's controls. Young and Wray clash over what to do with the Alliance prisoners.

The crew encounters a ship remarkably similar to Destiny, which may hold the key to their returning home.

Young is plagued by mysterious dreams where Destiny is destroyed by alien attackers no matter what he does.

Rush and Young investigate an abandoned alien craft which is just outside the Destiny. While they do this, the crew onboard the ship find the bridge and discover that Rush is responsible for the countdown clock not activating when the ship emerges from FTL.

Simeon makes his escape from Destiny, sending Nicholas Rush on a vengeful mission. But Young and Greer attempt to retrieve Simeon unharmed.