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.

As Young and Camille attempt to resolve the hostage crisis with Kiva, Destiny suffers from power fluctuations and blackouts due to its proximity to a binary pulsar.

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.

The crew's new-found control over Destiny's flight path introduces new risks when they find themselves in the middle of a war between two races.

Locked in a battle with a Drone Command Ship, the Destiny is surprised by the arrival of the Aliens that abducted Rush and Chloe.

An alien creature attacks an exploration team from Destiny, taking two crew members captive.

Eli and Rush have found a way to identify the location of drone mother ships using the Destiny's long range sensors. The bad news is that the Drones seems to be awaiting them at every possible stop along Destiny's path. They find a temporary solution to neutralize the mother ships but realize that they cannot engage in a major battle every time they need to re-supply. Eli suggest that they use the stasis pods for the crew and jump to the next galaxy, a trip that will take three years. All goes well until they realize that one of the pods has been damaged and one person will have to stay behind in the hopes of fixing the unit in the short time available or die.