Troubled by nightmares of her abduction, Chloe turns to Rush for understanding. The two discuss the matter and agree that the ship will never be safe.
In a tense discussion between Young and Rush, Young accuses the doctor of causing the connection to the aliens by stealing a communication stone. Rush tells Young that he has learned that the aliens have been tracking Destiny since long before this crew arrived onboard. On Rush's suggestion that there may be a tracking device somewhere on the hull, Young orders Eli to search the outside of the ship with a kino, and an alien shuttle is found. Scott and Young take one of their own shuttles to blast the enemy craft off the ship.
Tensions between the civilians and the military are mounting, however, and Wray and Rush continue their plan to wrest power from Young. As Scott and Young are in the shuttle, Rush begins a process to transfer control of all systems to a satellite control room just before the ship jumps into FTL. This plan has an unforeseen side effect: Young's shuttle won't lock into its dock, and if the two military men are caught outside during the jump, they and the shuttle will be vaporized.
Chloe has also been part of planning the coup, and she and Wray convince Rush to stop the power transfer and save Scott and Young. He does so, but in the process loses his objective: He has only gained control of the food and water systems. He seals the bulk of the military personnel on one side of the ship - with Eli in the main control room - and delivers his demands that Young yield all weapons and submit to a civilian government. Young is aware of the stalemate, but shrewdly accepts a deal of a limited amount of food and water in exchange for Eli. Letting the insurgents think they have the upper hand, he and Greer prepare to attack via the hole the aliens cut in the ship when they abducted Chloe. The two don space suits, but as they're making their way across the ship's hull, two alien shuttles appear.
In a panic, Eli demands to know how they found Destiny. Rush reluctantly tells Eli that the aliens implanted a tracking device near his own heart. Not wasting any time, he orders Eli to help him harness all the ship's power and direct it into the defense shields. Young and Greer make it back inside the ship and the shields go up just as the enemy opens fire. Safe on the other side, Greer reunites the military forces, and things get violent, fast.
Wray finds out about Rush's chip just as Young arrives on the scene. They convince Rush to have it surgically removed - Chloe will switch consciousnesses with a doctor on Earth to perform the surgery. Just as she's about to remove the tracking device, however, the shields begin to weaken and the connection is broken, leaving TJ to complete the surgery on her own. She succeeds, and the shields hold out long enough for the ship to make its next jump, but things will never be the same between the military and civilians onboard.