Still in the grips of the Lucian Alliance, with Colonel Telford, Kiva, and TJ wounded and unconscious, Colonel Young attempts to win back control. Scott and Grier manage to shield themselves from the pulsar blast by taking shelter in a crevasse of the ship, and Eli couldn't be more relieved to see them when they finally make it in. Their joy is eclipsed with wonder, however, when Chloe, mysteriously recovered from her gunshot wound, joins them. Once reunited with Rush and Brody, Rush fills Eli and Chloe in on a new development: the ship's shields are now strong enough for them to jump away. But Rush has another idea: he'll divert power from the shields in order to threaten the Lucians into returning control of Destiny.
TJ, meanwhile, has an eerie experience that she is back on the planet that the aliens built, with Caine - and her baby is safely delivered. But she soon learns that the nebula that delivered her to safety must take her back to the ship - these are the rules instituted by the aliens who built the planet.
Varro convinces Young to take his people to a nearby, barely hospitable planet. Lucian infighting leads to Dannik wresting control from Varro just after they learn that Kiva succumbed to her wounds. Dannik sends Varro and any soldiers loyal to him after Young on the nearby planet. But when Rush reveals his trump card, the Lucians set out for blood. Grier and Scott attempt to find TJ and bring her to the fortified zone of the hydroponics room with Rush and the rest, so that the next pulsar blast will kill only the Lucians.
Dannik is unyielding, and the entire population of Destiny seems doomed, but Ginn, the engineer, steps in to restore peace by burying three bullets in Dannik's back. Rush and company reclaim control of the ship, and bring back the passengers - Earthling and Lucian - from the nearby planet, and the ship jumps to safety.
And TJ, after several long, hard talks with Caine, is suddenly transported through the nebula back to Destiny. She regains consciousness to find more confusion: no one aboard perceived her as being gone, though her baby is. But she sees one reassuring sign: the same nebula that brought her to the planet is just outside the window of Destiny.