Season 2
Episode 1: Intervention
Original Air Date—28 September 2010
The Lucian Alliance is still in control of the Destiny and Col. Young is determined to get it back under his control. Young and most of his personnel are prisoners however leaving it to Rush, Lt. Scott, Sgt. Greer, Elia and Chloe to find a way to get control of the ship. They are left alone on the Destiny when Young and the prisoners are dispatched to a nearby planet. When they take possession of the control room, Rush devises a plan that will likely result in the death of the Lucian Alliance members but also any of their colleagues that might still be on board. Meanwhile, TJ is unconscious recovering from her wounds but seemingly awakes in a perfect where she and her newborn are joined by crew members from the past.
Episode 2: Aftermath
Original Air Date—5 October 2010
Col. Young and Dr. Rush are back in control of the Destiny and the remaining members of the Lucian Alliance are in custody. They're not proving to be very cooperative however and trouble looms. Of greater concern is the lack of food and water on board. Rush brings the Destiny out of hyperspace - he now has complete control of all of the ship's data banks, a fact he has not shared with anyone - near planet that may provide the supplies they need. The expedition to the planet's surface is an a shuttle - it doesn't have a working gate - leads to tragedy and the death of a crewman. Rush is also having a strange experience on the command bridge he has found.
Episode 3: Awakening
Original Air Date—12 October 2010
The crews comes across a ship that is virtually identical to the Destiny. The two ships automatically dock with each other and begin transferring data between systems. No one appears to be aboard the new ship but Scott and Greer discover a hold with a series of gates, presumably being transported to various sites. The scientific team thinks that combining the power of the two ships may allow them to open a gate to Earth. It all goes wrong however when the new ship begins to drain the Destiny's power. Nor, it turns out, are they alone on board the new craft. Meanwhile, Col. Young continues to clash with the remaining members of the Lucian Alliance who want to be freed from custody. Several of the civilians think he should give them a break but he's convinced they're a threat. TJ is still dealing with her emotions over the lost of her baby.
Episode 4: Pathogen
Original Air Date—19 October 2010
Eli rushes back to Earth using the communication stones when he receives word that his mother is hospitalized and in declining health. She's stopped taking her medication and is clearly depressed over the fact that Eli has never been in touch with her. Eli has to decide whether or not to tell her the truth. Camile Wray also visits Earth to spend time with her partner, Sharon Walker, but something is clearly wrong. Chloe has been out of sorts lately and begins sleepwalking. A concerned Lt. Scott finds something startling in her diary. Col. Young decides the release the Alliance members from the brig but one of them is having difficulty fitting in.