As Brody works on the still, Rush tries to explain that the structure signal they're looking at is the biggest mystery of all time. They'd rather get some alcohol from Brody once he fixes the still, and Rush gives it up as a lost cause.
comes out of hyperdrive and Young checks with Volker on the bridge. They spot the shuttle outside: the one they left behind on the alien construct planet. Young and the others gather on the bridge and Dr. Robert Caine hails them on the radio. He identifies himself and asks what they should do. Rush points out that the shuttle couldn't have got through the atmosphere, much less made it across millions of light years, and Caine admits that he and the others, all seven of them, have no idea how they got there.
Eli insists that it's impossible that the shuttle could have found them, and warns Young that the aliens who built the planet from scratch can easily impersonate Caine. They figure that they need a working shuttle and Rush suggests they invite them aboard and take every precaution. Young has Scott talk them through the docking procedure.
Johansen gets word and runs to meet them, and complains that Young didn't tell her. He insists that what she experienced was a simulation, but Johansen believes it was more than that. Young warns that nobody mentioned a child, but Johansen insists she needs to know.
The shuttle docks and the eight others come aboard. Young has Greer and his men escort them to a private holding area, despite Caine's objections. Johansen notices Peter and Val from the planet when they watched over her daughter, but they only casually nod to her. She then runs into the shuttle but there's no sign of her daughter.
Eli records a kino message saying that they're losing Chloe and there's nothing they can do to stop it.
Scott goes to see Chloe in her quarantine chamber and tells her what happened. She realizes that he no longer considers her the person she once was before the transformation began. Chloe shows him that the transformation has spread, and said that they're past the point where she can resist.
Young talks to Caine via the kino, and Caine says that the last thing he remembers was closing his eyes aboard the shuttle during the winter. Caine suggests that God may have delivered them, but Eli doesn't buy it. Young says they'll be examined one at a time to make sure they're safe.
Scott and the others check the shuttle and inform Young that it is brand new, as if had been rebuilt from scratch. Johansen finishes her exams and tells Young that all eight are in the same condition they left them, but have no memories of their time on the planet. The others think the aliens returned them as a sign of benevolence, but Young doesn't believe it. He admits that he feels uncomfortable around them, and Johansen confirms she feels the same.
Chloe records a message saying that she isn't sure how long she'll still be herself. Eli suggests she make her goodbyes, starting with him because it'll be the easiest, but she takes offense and says that it isn't that easy. Eli tells her to continue and she goes into a trance.
Young releases the others and tells them that they'll be given jobs to perform. Caine wonders at the hostile welcome, but Young merely says not to give him a reason to treat them as prisoners.
One of the others, Rachel, goes to see her friend Morrison. He quickly gets away from her, telling her not to touch him. Greer and Camille notice, and Greer admits that he had written off the scientists due to their lack of survival skills. He has never had anyone come back until now.
Johansen talks to Caine and offers to show him their expanded hydroponics bay. She asks him about her memory of being on the planet, which the others called Eden, and her daughter was there. She explains that in her memory, they were living in cabins provided by the aliens, and Caine said he would take care of her daughter. Caine doesn't remember any of that.
Camille tries to get Peter to remember anything momentous on the planet, but all of his memories are of gathering food and fuel. She then shows Young tapes of the interviews and concludes that the aliens tampered with their memories. However, she insists that they are still their people, and agrees to keep at them.
Greer meets Scott in the hall as the latter goes to see Chloe. Scott realizes that something is wrong, and insists that it would help if some of the others came to see Chloe. Greer reminds Scott that she's in quarantine for a reason, and he's there to make sure that Scott doesn't make mistakes. He admits that he prays for Chloe every night, but she's turning into the enemy and the day will come when they have to eliminate her.
In the mess room, Eli comes over and makes small talk with Val. She says that she's starting to have flashes of memory. She mentions how she went skinny-dipping on the planet, but then rubs at her head in pain. Her nose starts bleeding and she screams in agony, and then falls over, bleeding from her skull.
Caine comes to see Rush on the bridge. Rush has confirmed that the shuttle teleported instantly from the planet to the ship without traveling across the intervening distance. Caine asks about the signature they've found, and wonders if it's the Hand of God. Rush insists on defining it in scientific terms, but Caine figures that God saved them for a reason. In response, Rush wonders what the reason is, since they have no memories or proof of what happened to them. Angry, Caine starts to leave, but Rush asks why the alien restored the shuttle in pristine condition, but the humans without their memories. He suggests that it wasn't God that brought them there.
Young summons Caine to the infirmary, where Johansen has confirmed that Val died of extreme head trauma, as if something heavy slammed into her skull. Caine doesn’t understand, and Camille suggests that she use hypnotic regression to stimulate their memories. Young agrees and Caine goes to tell the others about Val's death. Johansen warns Young that she's not handling the situation.
Greer comes to see Chloe, and reluctantly tells her that Young will eventually eradicate her as a threat, and he'll be the one to do it. He insists that he couldn't let it be anyone else, and asks for her forgiveness for when the time does come. Greer asks her to say the words, and she says that she forgives him. He thanks her, and she tells him to take care of Matt. Chloe wonders if she should tell him to stay away, and Greer agrees that it would be a good idea. He asks for the opportunity to say goodbye now, but can't let her hug him.
Chloe records a statement to Scott, saying that she wishes she could have introduced him to her friends and family. She asks him to forgive Greer for killing her, and that she wouldn't have wanted anyone else to do it.
Camille regresses Peter, who talks about how they were struggling against the coming winter and trying to gather food and fuel. He and Val fell in love, and they kept it secret from the others. Caine advised Peter to give it up and prepare for winter, but he refused and went into the forest to chop firewood. He inadvertently brought the tree down on Val, crushing her skull. Peter comes out of his trance and remembers that Val died on the planet. He then collapses, twitching in agony. By the time Johansen and Young get there, he's dead.
Johansen conducts an autopsy and determines that he died of dehydration and hypothermia. She suggests that the others are dying again, in the same order they died on the planet. Young has his men bring Caine and the others to the infirmary. Scott and Greer go to Rachel's quarters and discover that she's dying of malnutrition. Scott picks her up and carries her, going against Greer's advice. As Scott goes into decon, Caine arrives in time to watch Rachel die. Young demands answers from him, and Caine says that he's going to undergo hypnosis with Camille. When Johansen says that it isn't Caine's fault, Young points out that she would have met the same fate if she stayed.
Once he leaves decon, Scott goes to see Chloe and tell her what's happening. She tells him to get out. He does so, but promises to come back later.
Johansen and her team struggle to keep the four remaining others alive.
Camille regresses Caine, who describes how winter came and they took refuge in the shuttle. When the power systems broke down, they had to leave the door open for air. Peter is the first to die, giving up and walking out into the storm one night. Camille takes him to the last night before they work up in the shuttle, and Caine talks of how the others have all frozen to death. All he can do is pray. Then he woke up on the shuttle. Caine comes out of his trance, and says that he'll be dead before they come out of FTL. He remembers the moment of his death.
James finds a kino in the shuttle and gives it to Eli.
The four remaining others have died in their sleep, leaving Caine as the only one. Johansen figures that whatever the aliens did was temporary, and they reverted back to the state the aliens found them in. Johansen apologizes and Caine assures her that it's not her fault. He asks to go to observation deck one last time to see the stars, and asks Johansen to come with him.
On the deck, Johansen suggests that the aliens may have brought him and the others back so they could look on the stars one last time. Caine realizes that he's a reanimated shadow, an empty shell, and that God had nothing to do with it. He figures that the crew sensed his lack of a soul, but Johansen insists that she doesn't feel that way now. She wonders if he still believes, and Caine figures that his soul has moved on and is looking down to see how kind she is to comfort a shadow. He tells her that the greatest gift she can give her daughter, and the others, is to embrace Destiny
The crew gathers to watch the kino, which Caine used to record his last moments. They watch as he begs for help, and a blinding white light fills the shuttle.