Chloe has a nightmare of her abduction by the aliens, where she’s taken aboard their ship and locked in a liquid tank. Her mother watches her as Chloe pounds on the side of the tank, and she finally wakes up, next to Scott in his bed. He tries to reassure her and suggests that she talk to Johansen, but Chloe ignores him and goes for a walk. She goes to see Rush in the mess room, and talks to him as the only person who has experienced the same thing. They discuss the fact that the others think that they’re safe from the aliens, but they know better.
Rush goes to see Young, but the colonel wants to talk about the communication stones. Young figures that Rush kept one of them for himself when and turned the others over, and that he had it on him when he went to the planet and Young stranded him. Young then connected with them when he tried to use the stone. Rush doesn’t confirm his speculation, but suggests that the aliens are using a subspace tracking signal aboard one of their ships that attached itself to the hull of [I]Destiny[/I]. When Young asks him how he knows, Rush says that he caught images from the aliens’ minds while they were scanning his mind that indicate they’re obsessed with the Ancient ship. They’ve emerged from FTL and Rush suggests that they examine the hull and find the aliens’ ship.
Eli sends a Kino out to start scanning the hull, and Young meets privately with Greer. Greer voices his support for Young stranding Rush, but the colonel doesn’t confirm his speculation. They receive word that Eli has found the alien ship, attached to the hull, and Young leaves with Scott in the shuttle to destroy the ship before the [I]Destiny[/I] reenters FTL in an hour. As they go, Young notices Chloe and Rush talking together.
Rush goes to an isolated laboratory and meets with Camille. He explains that he can transfer all ship’s functions to the lab and that now is the best time to begin their plan. Camille reluctantly agrees and he tells her to get everyone into position.
Chloe come to Eli in the control room and asks him to show her the alien ship. They discuss how long the ship has been attached, and Chloe suspects that Rush has known about its presence for some time. Young and Scott destroy the ship and Eli assures Chloe that the aliens can’t track them, but she doesn’t seem sure.
In Hydroponics, Brody is working when Volker calls to inform him that they’re going with the plan ahead of schedule. Johansen makes an unscheduled visit and Brody conceals the radio before she can notice.
Young and Scott dock the shuttle but discover they can’t engage the clamps. The door won’t open and they call Eli, who confirms that they’ve lost control of the systems. A seemingly surprised Chloe checks the systems and they realize they’ve been locked out. The [I]Destiny[/I] will go back into FTL in seven minutes and the shuttle will be destroyed if it’s not attached to the ship inside of the shields. As Eli works to regain control of the systems, Young calls Eli on the radio but gets no response. The colonel tells Greer to find Rush. Meanwhile, Chloe runs to the lab and tells Rush what is happening. Rush reluctantly calls Eli and informs him that he’s interfering with Rush’s efforts to transfer control. He tells Eli to let him gain full control so he can dock the shuttle, but Young orders Eli to ignore the scientist.
With time running out, Camille tells Rush to stop the control transfer. He warns them that if he does, they’ll have given themselves away for nothing. Chloe insists that no one was supposed to be hurt, and Camille warns that they’ll lose the support of the other civilians if anyone is killed. Rush finally aborts the control transfer and Eli docks the shuttle just as the [I]Destiny[/I] goes into FTL. As Greer and his men approach their section of the ship, Rush uses the control he has to seal off all the doorways giving access.
Volker comes to Hydroponics and tells Brody what’s going on. When Johansen notices, they tell her that she wasn’t supposed to be there. Johansen goes to investigate and discovers that another military man, Airman Dunning, is caught in the civilian section and is holding several of Camille’s people at gunpoint. Camille arrives and apologizes, admitting that a few people were caught behind the lines. Johansen orders Dunning to stand down and Camille has her people lock them up for now.
Young contacts Rush, who points out that he now controls most of the ship. Eli realizes that they still maintain control of the life support systems, and Rush admits that he’d hoped Eli wouldn’t notice. Rush calls upon Young to surrender and let Camille take command. When Young threatens the civilians with loss of life support, Rush notes that they have enough air to last at least three days, which is as longer as the military personnel can survive without water. He warns that they’ll have to see who will break first, but it won’t be pretty.
As the standoff continues, Rush informs Camille that Young hasn’t cut off their air. However, he admits that Young has one thing that can break the stalemate.
As Eli tries to bypass Rush’s lockout program, Young assess the situation. He confirms that Johansen and Dunning are with the civilians, and the few civilians in the military areas know nothing about the coup. Eli is surprised to hear that Chloe is with Rush and Camille. Rush then offers them a trade: limited food and water in return for Eli delivered to them. Scott objects but Young has already agreed, while assuring them there’s another way in to the civilian area.
Eli goes alone and the civilians take him. As Chloe takes him to Rush, Eli asks why she’s working with Camille, and wonders if she came to the control room to distract him. Chloe claims that she didn’t know that Rush and Camille were going to start the plan so soon, and explains that she’s supporting Rush and Camille because Young left Rush to die.
The ship emerges from FTL and Young suits up with Greer. The two of them go out on the hull and prepare to spacewalk to the hole the aliens cut in the ship earlier.
In the mess room, some of the civilians complain about Camille giving food to the military, but she insists they need to stick together until Young accepts the inevitable and yields to civilian control.
Eli meets with Rush, who explains that he needs Eli’s help to boost the shields.
As Young and Greer make their way to the hull breech, three alien ships emerge from FTL and close in on the [I]Destiny[/I].
Rush admits that there is a second tracking device: the aliens implanted it near his heart while he was their captive. He’s already confirmed that Chloe doesn’t have a similar device. Rush explains that the aliens have been tracking [I]Destiny[/I], but the ship’s automatic shielding has protect it. Now the aliens are attacking in the hope that the newly arrived human passengers will make a mistake. Eli realizes that if he boosts the shields, Greer and Young will be unable to enter. He tries to stall for time. It doesn’t work for long, but Young and Greer manage to get inside before Rush boosts the shields. Young sends Greer to let in Scott and his team while he looks for Rush.
Chloe visits Johansen and Dunning. She insists that Young will soon capitulate, but Johansen warns her that the colonel is an experienced officer and will soon take back the ship. The aliens launch their attack as the civilians look about nervously.
Greer knocks out the civilian guards and lets in the rest of his team. Scott tells his soldiers to make sure not to permanently harm anyone.
Chloe insists that Camille and Rush can handle the aliens, but Johansen warns her that she can’t trust Rush. Chloe insists that it was Rush who saved her while Young was willing to destroy the alien ship and her along with it. Scott arrives and is shocked to see Chloe with the other civilians. He frees Johansen and Dunning and then leaves Chloe behind.
Camille arrives in the lab and Eli tells her about the tracking implant. She wonders if Rush is working with her because he feared that Young would try to kill him again. Young captures them while the military get to the mess room and secure the other civilians. James hits one and Greer is ready to shoot Volker when the scientist hesitates.
Eli tries to get the weapons online but Rush notes that he created a secondary lockout code. Young is ready to shoot him when Scott and the others arrive. Young reluctantly lowers his gun and Eli tells him about the hidden transmitter. Young tells Johansen to remove it despite her lack of qualifications, and they have no choice. He tells them to use the communication stones to bring in a doctor, and Chloe volunteers to make the switch.
After establishing contact with Earth, Dr. Brightman switches with Chloe and prepares to operate on Rush. Johansen provides what assistant she can. Meanwhile, Eli bypasses the lockout but warns that they don’t have enough power for weapons and shields. He suggests that they follow Rush’s plan, maintain power to the shields, and withstand the alien fire long enough to jump back into FTL.
Brightman locates the transmitter in Rush’s chest and prepares to remove it. However, Chloe suddenly finds herself back as alien fire scrambles the communication stones’ signal. With 60 seconds left until they jump, Johansen is forced to take over and manages to remove the implant. With the shields falling, the [I]Destiny[/I] jumps into FTL in time, and Scott crushes the implant so the aliens can’t follow them.
After things settle down, Young orders the civilians to return to their quarters. Greer notes that they don’t have personnel to watch all of them, and Young tells him that it’s over. When he and Camille decide what to do next, she points out that he shouldn’t have abandoned Rush. Young admits that he’s right. Once she leaves, Greer argues that it isn’t over, and Young has to agree with him.