Chloe is walking through the empty rooms and corridors of Destiny and finally comes to a door. She looks through the window and sees herself on the other side, being abducted by the aliens. Chloe relives her abduction and watches as her mother arrives, and then an alien. Waking up from her nightmare, Chloe finds herself next to Scott in his quarters. He suggests she talk to Johansen, but Chloe refuse to let him help and goes for a walk. She finds Rush in the messroom, and he sympathizes. Chloe wonders what the aliens did to them, and figures that they're not safe no matter what the others think. Rush agrees with her.
Rush goes to see Young and talk. Young wants to discuss the communication stones and figures that Rush kept one for himself, and kept it on his person. When the aliens abducted him, they used it and that's how Young ended up in contact with them. Rush doesn't try to deny it, and would rather focus on how the aliens found them. When Young suggests they tracked the stone's signal, Rush doesn't believe it and suggests a subspace tracking device, attached to the hull of Destiny. He explains that he's been having flashes of mental images since they scanned his mind, and they've been tracking the Ancients' ship for a long time. Since they've emerged from FTL, Rush suggests they examine the hull and confirm his theory.
Eli sends a Kino out onto the hull and begins searching for the alien ship and its tracking device. Eli warns that it'll take a while and Young tells him to keep him posted. The colonel goes to the messroom and Greer asks to meet with him in private. Greer agrees that they were better off without Rush, but Young doesn't confirm his suspicions. Rush radios to tell Young that they've found the alien ship on the underside of the ship. As Young and Scott prepare to take a shuttle out to remove the device, Scott notices Chloe talking with Rush. They have an hour until the Destiny goes back to FTL, and Young figures they have plenty of time.
Rush takes Camille to a research lab and explains that they'll never have a better time. He tells her to get her people into position.
Chloe comes to see Eli and asks him to show her the alien ship. Eli admits that even Rush doesn't know how long it's been on the ship, but Chloe figures that he knows.
Scott and Young open fire on the alien ship and destroy it.
Eli tells Chloe that the aliens can't get to them, but Chloe doesn't appear convinced.
Brody is working in Hydroponics when he gets a call from Volker, who informs him that the plan is on. He's surprised and then notices Johansen as she comes in ahead of schedule, and ineptly explains why Volker was calling him.
Young and Scott dock the shuttle but discover that they've been locked out and the docking clamps refuse to engage. They call Eli, who discovers that he can't gain access to the systems. Chloe checks the systems and they realize that Eli has been locked out of the systems. He warns Young that when they jump to FTL in seven minutes, the shields won't cover the shuttle and it will be vaporized.
Young tells Eli to work out who is transferring the controls and how. With five minutes left, Young calls Rush but gets no response. He then calls Greer and tells him to take a detail to find Rush. With four minutes left, Chloe finds Rush and tells him that the shuttle clamps won't engage. He insists that they can't stop, but finally gives in and tells Eli that he has to stop interfering with the transfer control process. Once he does, Rush can lock the clamps. With two minutes left, Young orders Eli to continue trying to stop the transfer and ignore Rush.
Camille arrives and learns of the situation, and tells Rush to stop. Rush warns that if they stop now, their position will be compromised, but Chloe and Camille both tell him to stop. He finally gives in and aborts the control transfer. Eli locks the docking clamps just as Destiny enters FTL.
Rush uses what control he's gained to lock out Greer and his detail, and confine Young and Scott as they come back onboard.
Volker comes to see Brody, who explains that he shut off his radio because Johansen is there. She notices them talking and they admit that she wasn't supposed to be down there. Johansen finds Airman Dunning, pinned down by civilians, and Camille arrives to inform them that they're on the wrong side and the civilians have taken control of the ship. Dunning threatens Camille with his gun and asks Johansen what he should do. She tells him to put the gun down and Camille insists it will soon be over.
Young radios Rush and tells him that he won't get away with it, but Rush assures him that what's done is done. He has control of all accessible systems, including food and water. Eli informs Young that they have control of one key system: life support. Rush tells them that they want the military to hand over their guns and submit to civilian authority. Young notes that they have control of life support, but Rush informs him that they have more air as well as the hydroponics lab. They can survive at least three days, which as long as the military can survive without water.
Rush briefs Camille on the situation, noting that Young hasn't cut off the air. He warns her that Young still has one thing that will make a difference.
Eli tries to bypass Rush's lockout program, while Young confirms that Johansen and Dunning are with the civilians. The civilians they do have claim to know nothing, and Young tells Eli that Chloe is with the other civilians. Rush has offered a trade: limited food and water in return for Eli, and Young has already agreed. Scott advises against it, but Young says there's another way in.
Eli goes to the designated spot and confirms he's alone. Chloe escorts him into the civilian section and Eli asks why she's working with Camille. He suspects that when she came to the control room, she was trying to distract him. Chloe denies it, saying she didn't know when Rush was going to start his plan. Eli is surprised that Chloe is siding with Rush, but she notes that Young left Rush to die.
Destiny emerges from FTL and Young and Greer suit up to enter the civilian section through the hole the aliens cut in the hull.
Brody and some of the others disagree with Camille's decision to give the military some food or water. Camille insists that they need to stick together until Young accepts that he'll have to follow civilian authority.
Chloe takes Eli to Rush, who says that he needs Eli's help. They need as much power as possible to boost the shields.
As Young and Greer walk the hull , they look up and see the alien ships emerge from FTL near them.
Rush explains to Eli that there's another tracking device, surgically implanted in his chest next to his heart. Only Chloe knows about it, and Rush has confirmed that she doesn't have an implant. He prepares to dial up the shields, but Eli suggests they use weapons. Rush hopes that the aliens will realize they can't get through the shields. The ship's automated defenses have been repelling the aliens all along, and now the aliens hope that the new crew will make a mistake. Eli tries to delay him from activating the shields.
Young and Greer enter the civilian section before Rush activates the shields. Greer goes to open a door while Young looks for Rush.
Chloe comes to see Johansen and Dunning, and Johansen warns that Young will quickly take back the ship. They hear a rumbling noise and realize that the aliens are back and launching an attack.
Greer lets in Scott and the others, stepping over the civilians that he rendered unconscious. Scott orders his people to be as gentle as possible.
Camille comes to see Rush and Eli updates her on the situation.
Chloe insists that they're prepared, but Johansen warns that she can't trust Rush. The girl notes that Young was willing to sacrifice her, and it was Rush that saved her. Scott arrives and frees Johansen and Dunning, and then walks away with his team.
When she learns about the tracking implant, Camille wonders if Rush thought that Young would abandon him again. Young arrives and takes them captive, while Greer and his men capture the other civilians and force them to kneel.
Young orders Eli to get the weapons online, but Rush warns that he created a separate lockout code. When he refuses to obey the colonel's orders, Young prepares to shoot him. However, Young finally yields. However, Eli informs the colonel about the transmitter. Young tells Johansen to remove it, but she warns that she's not qualified for it. When Rush objects, Young points out that he has to do it and suggests they use the communication stones. Chloe volunteers to provide a body for the surgeon from Earth.
Dr. Brightman comes through form Earth via the communication stones and Johansen provides what equipment they've improvised from the materials they have.
Eli finds a way to bypass the lockout, but warns Young that they can't spare the power to fire back. He believes that they can sustain the shields and resist the alien fire long enough to jump.
Brightman finds the transmitter and prepares to remove it… and Chloe is back. Scott informs Young that they've lost the connection. There's nothing Eli can do, and they have a minute left. Johansen has no choice but to take over and they have to resedate Rush as he wakes up. She does what she can and manages to remove the implant. Scott destroys it and informs Young.
As the shields fail, Destiny goes into FTL just in time.
Young sends the civilians back to their quarters. When Greer warns that they can't guard all of them, Young tells him that it's over. He then turns to Camille for suggestions, and she insists that he shouldn't have left Rush on the planet. Young agrees with her. Once she's gone, Greer warns that it's not over and the colonel agrees.