A teenager, Jonah Bevan, is walking along a barrage in Cardiff when his mobile phone rings. His mom has left him a message saying he's nine minutes late. He looks across to the apartment where his mom Nikki waves. As Jonah continues on, the wind picks up and light flares from above. Seconds later his phone drops to the ground as he vanishes.
Seven months later, PC Andy calls Gwen in to investigate Jonah's disappearance. He relates the night of the disappearance and what Nikki saw. Gwen is more interested in knowing why Andy didn't come to her wedding even though he had the time off. He admits he can't let it go and have her pledge her life to Rhys, and thinks she can do better. She thought he had overcome his feelings three years ago and Andy turns the conversation back to Jonah. He says he was the first one there, and sat with Nikki. When Gwen wonders if there was anything strange, Andy suggests that she should know. He shows her the CCTV footage which reveals that Jonah simply disappeared within a six-second timeframe. Andy thinks Gwen knows all about it and then shows her additional footage from 45 minutes later, showing Jack was on the bridge.
Gwen checks with Tosh, who has no record of rift activity on the barrage or in the vicinity on the night in question. Jack says he was visiting a coffee shop in the area and claims to know nothing about Jonah's disappearance. He offers to help investigate but Gwen turns him down, and he leaves to go Weevil hunting with Ianto.
Later, Gwen meets with Andy, who thinks that they're covering things up. She insists that she'd tell Andy if she knew anything, and he accuses her of no longer caring about people. Gwen goes to see Nikki, who told her that Gwen might be around. She explains that she's been obsessively watching tapes of crowd footage in the hopes of finding her son. Nikki talks of how she often sleeps in Jonah's room and keeps his diary for him, imagining that he's there. She asks Gwen what she did wrong and wonders if she was too nosy, or too uninvolved, or didn't love him enough. Nikki only knew Jonah's father for six weeks, and he never showed up when Jonah's disappearance was first on the news. She invites Gwen to a support group for missing people that she's set up and Gwen promises that she'll try to get there.
Gwen comes home three hours late and Rhys complains that it's been the fourth time, and she's avoiding the discussion he wants to have about children. She asks him if he thinks she's changed and then admits that Andy still fancies her. Rhys finds it amusing and they end up in bed. The next morning, Tosh calls Gwen to inform her she's found some new data. Gwen goes to the Hub and Tosh explains that she found a negative rift spike. They've dismissed them as insignificant until now, but Tosh wonders if the rift can also take things and people as well as leave them behind. Gwen makes sure that Tosh hasn't told anyone, and asks her to keep it to herself for now.
Gwen meets with Andy, who thanks her for looking. They go to Nikki's Searchlight missing person meeting, but they're the only ones there. However, people start to come in and Gwen is taken aback at how many recent disappearances there have been. Gwen admits that it's too much and she can't help them all. Andy tells her to focus on Jonah but Gwen realizes that they're all part of her investigation. She runs back to the Hub and has Tosh cross-reference negative rift activity against the dates and times of all the disappearances. Gwen still wants to keep their investigation private until they're sure. They soon realize there are hundreds of such disappearances.
Gwen and Tosh take the data to the others, and demonstrate the disappearances correspond to negative rift activity. Gwen wants to find a way to prevent them, but Tosh admits she can't detect the spikes or predict them. Jack notes that there's nothing we can do and asks Gwen what they can do. She suggests they help those left behind but Jack says they're not qualified and Owen admits the families need counseling and support they can't provide. Gwen insists that they don’t have to be hard but Jack orders her to close it down. Ianto tells Gwen that he'll try to change Jack's mind, while Owen continues to support Jack.
Rhys and Gwen go to the park and Rhys tries to discuss his co-workers, and Gwen finally tells him to stop wittering. Rhys notes that she's been refusing to talk about children, but Gwen says that she can't have children as long as she works for Torchwood due to the job requirements. Rhys snaps at her and asks her what she's fighting for. He points out that she does her job so people can have normal lives, and asks if she thinks her job is more important than real life. She apologizes but he tells her to keep her work problems at work and sort them out there.
Gwen goes back to the Hub and walks in on Ianto and Jack making love. Once she recovers, she tells Jack she's not going to let Jonah's situation go and she's taking it on as a personal project. Jack orders her not to and refuses to explain further. After he goes, Ianto tells Gwen that there's a package on her desk. Inside it is a seemingly high-tech unit. She calls Andy and arranges a meeting, and he explains the unit is a GPS. A deserted island in the middle of Bristol Channel is listed, Flat Holm Island. As Andy gets coffee, Gwen calls Ianto and asks if he left her the package. Ianto refuses to answer and hangs up. Andy comes back and says they'll hire a boat and poke around the island in the morning. Gwen tells him that she's going out alone but Andy insists that he's part of it. He then asks if there are any vacancies at Torchwood and wonders if they want to hire him. Gwen dodges the question.
Gwen returns home and discovers that Rhys has left pillows and blankets out for her to sleep on the couch.
The next morning, Gwen meets Andy and he asks her to get some tea. As soon as he leaves, she pays the captain extra to leave without Andy.
Once alone on the island, Gwen goes to the lighthouse and climbs to the top. She notices people walking toward some seemingly empty bunkers and Jack following them. She goes back down and follows them. Going in, she finds an intercom and buzzes. A woman at the other end asks who she is and Gwen gives her Torchwood ID and says she's with Jack. The woman lets her in and takes her through a corridor with cells and people locked inside. There's also a ward where a white-haired woman is nervously watching the telly. The woman, Helen, says that they all find it uncomfortable at first. Each door has a name written on it, and in one room, a man is sobbing hysterically. Gwen finally realizes that the names are of people who went missing due to the rift activity.
Gwen demands to know what's going on and Jack arrives. He offers to explain and Gwen backs away from him, and she sees the room where Jonah is kept. Gwen demands that he opens it and he does so. Inside, she finds a scarred and deformed older man in his 50s. The man explains that he's the Jonah that went missing on the barrage. He describes how he found himself on a distant planet covered in flames and a man rescued him. The man managed to save him and put him into a rescue craft. As they departed, they watched as the entire solar system burned. Gwen apologizes for what happened to him and Jonah asks if he can trust her to tell the truth. She takes his hands and he asks if he's really home. Gwen assures him that he is and he thanks her. She tells him that her mother has been looking for him for the last seven months, and that he's safe now. Jonah asks her to bring Nikki there.
Outside, Jack explains that there were two persons like Jonah locked in the vaults when he took over Torchwood. He set the place up and they now have seventeen "patients." The rift activity has increased over the last year. Jack explains that the missing persons are badly damaged, and all they can do is care for them. Gwen insists on bringing Nikki there but Jack wonders how they can possibly explain to Nikki. He wonders what Gwen will do if Nikki doesn't accept the truth about the rift and Torchwood, but Gwen insists that they have to tell her the truth, and she at least has to try.
Gwen goes to see Nikki and tells her that she's found Jonah and he's alive. Nikki breaks into tears and Gwen warns that there are things she has to know before she can meet her son.
Gwen calls Andy to tell him that she's found Jonah and needs Andy to verify what she's saying. Andy accuses her of using him and realizes that she never recommended him for Torchwood. Gwen insists they can make it right and Andy reluctantly agrees to help.
Gwen and Nikki go to the island and visit Jonah's cell. Nikki insists on seeing her son and goes into the cell. However, she recoils in horror and insists that he's not her son. Jonah asks about his the door in his room and describes things that they did together. Nikki finally accepts who he is and embraces him. He apologizes for being late that night and blames himself, but she says she'll be there. Helen tells Nikki that she'll have to leave Jonah there and Nikki refuses. However, Jonah starts to shiver and Helen warns them that Jonah is in a downswing, and his good phases get briefer every day. Jonah starts screaming… and screaming… and screaming. Gwen learns that it lasts 20 hours every day. He had looked into the heart of a dark sun and what he saw drove him insane.
A week later, Gwen meets with Nikki and tells her that she can visit when Jonah is in his good phase. Nikki asks Gwen not to do the same thing for everyone else, because now her memories of Jonah have been ruined. She admits that she was better off not knowing what happened to her son. Now she has no hope. There's nothing that Gwen can do except leave.
Gwen goes back to the Hub and takes down all the posters of missing persons.
Nikki puts away her tapes of all the crowds where she has looked for Jonah. She puts away his diary and takes down everything in his room.
At home, Gwen lights candles and prepares supper for Rhys. She says that tonight, they'll talk about having children, the future, anything he wants. Rhys asks if she's all right and hugs her as she bursts into tears. Gwen apologizes and they sit down together on the couch, and Rhys tells her to tell him everything.