On Destiny, Eli finds Chloe in the control interface room. She admits that she doesn't know how she got there, and the last thing she remembers was taking a nap. Chloe abruptly leaves. Eli talks to Scott and admits that she's been acting odd for a while. Scott admits that she's been withdrawn, but she hasn't wanted to talk about it. Before Eli can pursue the matter, Young comes over and says that he's needed on Earth because his mother is sick.
On the hidden bridge, Rush works without sleep and Gloria advises him that he needs rest. Rush manipulates the countdown clock to bring them out of warp and Franklin appears to warn him that he can't do the work on his own. Park and Brody call to tell him that they've come out of warp despite the fact there are no Stargates in range, and wonder where he is.
On Earth, Eli is informed that his mother has stopped taking her medication, and is suffering from depression, endangering her life. He goes in and claims he's Airman Tracy, the person whose body he's using. Eli explains that he couldn't make it but he's worried, and she points out that Eli isn't worried enough to be there himself.
Camille uses the communication stones to arrive on Earth and visit her girlfriend, Sharon Walker.
In his quarters, Scott asks Chloe where they're at, and if they would even be together if they weren't trapped on the ship. He tries to pursue the matter but Chloe shushes him.
Sharon and Camille have dinner, and Sharon drinks wine and insists that everything is fine.
Benson and her men release the Lucian prisoners on Young's orders. In his quarters, Young explains to Greer that the decision is made but that he's put an escort on each Lucian prisoner. Scott arrives to tell them that Chloe has disappeared.
Johansen and Benson are in the mess room and watch as the Alliance members come in. Simeon says something to Park, offending her, and Greer shoves him up against the wall and tells him not to talk to anyone. He has his men take Simeon back to the cargo hold, and then tells everyone that they need to form search parties to find Chloe.
On the bridge, Rush watches as the clock runs down and Destiny goes back into hyperspace. Gloria warns him that lack of sleep is making him careless, and two people have already died as a result.
Young comes to see Simeon, who apologizes and reminds the colonel of their deal. He promises to hold up his end of the deal.
Lt. James and her search party find Chloe in a cargo hold, prying at a sealed box. She calls Scott.
Sharon searches for her keys, much to Camille's amusement. However, when Sharon snaps at her, Camille realizes that something is wrong. Sharon finds her keys in the door and remembers that she left them there a day ago. She blames herself and then says she'll be back in an hour or two.
Eli comes back to see his mother, who wonders why Eli never calls her. He gets her to talk about her favorite science fiction movie, E.T., and tells her that it is possible to travel to other galaxies. Eli tries to explain about Stargates and finally admits that he's Eli in someone else's body.
Johansen examines Chloe, who admits she has no idea how she got to the cargo hold. Scott wonders if the aliens are using the communication stones, but Young confirms that they're clean. Johansen has Chloe stay overnight for observation.
Eli and tries to explain how the communication stones work, but realizes his mother doesn't believe him. She wants to know when Eli is coming home, and tells him not to call her "Mom." He describes the day that his father left, but she still doesn't believe him and calls for the nurse.
Scott goes through Chloe's diary and finds alien writing. He shows them to Rush and the others, and Rush realizes that it's the same language they found on the crashed hip. Rush is sure that Chloe didn't have any tracking devices in her, but suggests that some kind of genetic manipulation is gradually turning her. Young orders a quarantine until they know what's wrong, but Rush says that they can learn more by letting her roam freely.
Eli calls Camille to the hospital and explains that his mother is healing. However, he insists that his mother has given up mentally because she believes that Eli is gone. Camille insists that he needs to make her understand that she has to take her meds.
Scott accompanies Chloe until Rush takes over for the new shift watching her. Once he goes, Rush takes Chloe to a corridor and tells her to study the formulae that he's scribbled on the walls. She starts adding to the equations and finally finishes it.
Johansen comes to see Varro in his new cabin. He invites her in and apologizes for Simeon's actions, and Johansen says that Young has released Simeon... for now. She tells Varro that Simeon needs to work harder at getting along and leaves.
Scott finds Chloe and Rush in the Gateroom. Rush leaves and Chloe explains what happened.
Camille goes back to Sharon's house and tells her what happened, and notices that Sharon is drinking again.
Varro talks to Simeon privately, and Simeon warns that they'll be imprisoned again anyway once Young learns that they've been giving him false information. Varro tells him that he and the others have been truthful, and tells Simeon not to say anything.
Destiny comes out of FTL, and Brody and Park again realize there are no Stargates nearby. They try to call Rush without success, and call in Young to inform him what's going on. They figure that Rush is doing it, but don't know how. Brody asks for Eli, but Young says Eli is where he needs to be, on Earth. Rush comes in and claims that he was sleeping in his quarters, but Young already sent a man to confirm he wasn't there.
Rush takes Young, Brody, and Park to the corridor and shows them his equations. He tells them that the aliens influencing Chloe are studying everything they do, and then lies and says the aliens are using her to bring the ship out of FTL.
Scott is watching over Chloe when Greer and a squad of soldiers arrive to take her into custody.
Later, Simeon is walking down a corridor when Greer tells him to turn around. When Simeon questions his courage, Greer gives his gun to the other soldiers and dismisses them. Simeon turns and goes without a word.
Scott comes to see the imprisoned Chloe, who worries that she's slipping away. Scott assures her that they'll fix the problem.
Camille finds Sharon staring out into the night. Her girlfriend admits that she misses seeing the real Camille, and Camille explains that the few moments when they're together are what keep her sane. Sharon breaks into tears and they embrace.
Johansen monitors Chloe and tells Young that she can't detect any physical changes. She warns him that quarantine isn't a long-term solution, and Young admits that she's right.
Eli's mother wakes up to find him sitting at her bed. He asks her to wait before calling a nurse, and says that Eli is worried and he can't leave her there like that. She asks if she'll ever see Eli again, and Eli admits that he doesn't know. He goes and calls Camille, saying he can't go back to the ship with his mother in her current mental state. Camille has an idea and calls the authorities, and explains that they need Eli focused. When they balk, she tells them to do it anyway.
Mrs. Wallace finds herself aboard Destiny thanks to the communication stones. Eli is there, as himself, and she embraces him. He shows her a nearby planet, and promises that he'll find a way home. Mrs. Wallace tells him that she's proud of him.
Later, Eli tells Scott and Young that his mother is doing better, and thanks Young for letting his mother come there. Young says that he has to thank Camille. Rush calls to tell them he has a cure for Chloe: the neural interface chair. He explains that the chair has safeguards against non-humans using it, and it will eradicate the alien presence inside of her. Scott objects but Young asks Chloe, who agrees. She sits in the chair and Rush activates the program. It only takes a few seconds, and then Rush shuts it down. Johansen confirms that Chloe is stable, and Rush says they'll soon find out if it worked.
Eli comes to see Camille and thanks her for bringing Mrs. Wallace on board, as well as for understanding.
Scott and the others take Chloe back to her quarters, and stays to watch over her.
Sharon comes to see Mrs. Wallace at the hospital.
Rush comes to see Chloe and tell her what she's already realized: that she' s not cured.
Greer watches Simeon as he walks around the ship.
Camille sits in her quarters, alone.
Johansen watches Varro as he's escorted around the ship.
Chloe, Scott, and Eli talk in the mess room.
Gloria asks Rush if he can trust Chloe. He says that he can use her to solve his problems as long as he doesn't give away the alien presence within her to Young and the others. Chloe has to play along to keep her freedom.
Chloe lies next to Scott in bed, and stares at the ceiling with silver eyes.