Jack, Ianto, Owen, and Tosh track aliens to a building in the middle of nowhere. As they notify Gwen by radio to meet them, Tosh confirms the alien energy patterns don't match one they've seen before. They split up and Tosh and Jack detect one creature at either end of the building. As they split up, Owen and Ianto cover the other end. Each member finds an explosive device that goes off just as they find them.
At home, Gwen wakes up and discovers she has a text message.
As Jack lies buried in the rubble, dead, he thinks back to one thousand, three hundred and ninety-two deaths. He wakes up with a bottle thrust into his abdomen and pulls it out, and invites two women to give him a feel. He rambles on about how he isn't used to reviving. The ladies silently approach him and then chloroform him unconscious. He wakes up to a chair and they rip open his chest and proceed to torture him using electricity. Jack laughs as they note he's still breathing, and comments on their advanced technology. One of them shoots him in the head. He wakes up a few minutes later and they wonder why he's not dead. They then ask about the Doctor, quoting back transcripts of Jack saying that the Doctor can fix him. They explain that they're with Torchwood, which was organized to combat and other threats. Jack points out the Doctor is the one who saves them from threats, and then tells them that the Doctor left him behind, and he uses the rift to refuel the TARDIS. They refuse to let him go unless he joins Torchwood, and give him his first assignment.
Jack finds the alien, a Blowfish, and brings him in. The agents immediately kill the alien as a threat to the empire and Jack wonders if they'll do the same with him. They assure him he's safe because he's an ally now. They pay him and threaten to lock him up unless he continues to work with them. Jack considers it and then walks away and goes to a bar. A young girl offers to read the cards for him whether he wants to or not, and predicts that the one he's looking for is coming, but won't arrive until the 21st century. Jack realizes he has nothing to do but to work for Torchwood.
New Year's Eve, 1999, and Jack returns to the Hub to discover that one of his teammates, Alex, has killed the rest of the team. As he looks at a blue alien locket, Alex tells Jack that they're not ready, and he killed the others as a mercy. He turns the Hub over to Jack and then shoots himself before Jack can stop him.
In the present, Gwen brings Rhys and helps free Jack, who comes back to life. They start looking for Tosh, who is buried in the rubble.
Five years earlier, Tosh's boss at the Lodmoor Research Facility compliments her on working late and goes. Once he's gone, Tosh breaks into the computer room and accesses the system. She tracks the security guard and runs to a secure records room, ducking the cameras. She finds the top secret files she needs and hides them under her sweater, and then goes out past the security guard. At home, Tosh uses the stolen plans to build a sonic modulator. She goes to a building and meets with a woman and a man, and demands to see her mother in return for the device. They bring in Tosh's mother but warn that now she's proven herself, Tosh has so much more to give. They then torture Tosh and her mother with the sonic modulator. Soldiers burst in and arrest them, taking Tosh away before she can confirm if her mother is all right.
Tosh is placed in a cell and a woman informs her that she's in a UNIT facility and will be held indefinitely without legal representation or outside communication. They refuse to tell her if her mother is safe. Tosh waits for long days until she's told to prepare for inspection. Jack comes in and tells her they've wiped her mother's memories so she won't remember what happened. He warns her that they're going to make an example of her by keeping her without charge forever. Jack shows her the sonic modulator and notes that she easily built it. Further, the plans she stole didn't work. He offers to get her released in return for her working for him for five years. Jack tells her that he protects people, but it's a work in progress. She can only have limited contact with her mother. When she wonders why he would trust her, he says instinct, and then warns that it might be dangerous.
Gwen and Rhys find Tosh but they don't have enough strength to move the pillar trapping her. Rhys stays with Tosh while Gwen goes to find the others. As she starts to go, Rhys asks if it could have been her but Gwen says they don't have time to discuss it now.
Ianto tries to dig his way out of the rubble.
Twenty one months earlier, Jack battles a Weevil in the woods. It bites him, but Ianto arrives and starts clubbing it. Jack tackles the creature and together they manage to subdue it. Ianto introduces himself and then notices that Jack has stopped bleeding. He knows what a Weevil is but Jack says he doesn’t know what he's talking about and leaves with the Weevil.
Jack leaves the Hub and finds Ianto waiting outside with a cup of coffee. Ianto insists he wants to work for him, and Jack has already run a background check and isn't interested. He knows that Ianto works at the London Torchwood Institute until his girlfriend died. Jack insists he's severed all links with Torchwood London, but Ianto asks for a chance to prove himself. When he wonders what he should do about the memories of what he saw at Canary Wharf, Jack tells him that there's no job for him and never will be.
Jack is driving to an investigation and finds Ianto waiting for him. He threatens to wipe Ianto's memory if he stops stalking him and starts to walk off, but Ianto asks if he's going to help track down a pterodactyl that came through the rift. Jack agrees and they go to a warehouse where the creature attacks them. They track it down together and Ianto offers to be the decoy. He offers it chocolate and distracts it so Jack can inject it with a tranquilizer. It ends up grabbing Jack and flying him around. He injects it and it finally drops him on Ianto. The two stare each other in the face for a moment and Ianto starts to go, and Jack tells him to report to work the next day.
Jack and Gwen free Ianto and fix his dislocated shoulder. They admit they haven't found Owen yet, and Ianto warns them he can't heal.
Owen is trapped beneath a loose window pane that threatens to come down on him at any second.
Four years earlier, Owen is in bed with his girlfriend Katie Russell preparing for their marriage. Owen insists he'll marry her even if it kills him. As she makes tea, she briefly freezes up and starts having memory lapses. Later he meets with Katie's doctor, Jim Garrett, who warns that Katie has early onset Alzheimer's. Owen insists it changes nothing and they're going ahead with the wedding, and asks the doctor to run more MRI tests to confirm.
Katie undergoes the tests and afterward, worries that Owen will lose her. Owen assures her that he'll be there for her. Jim tells them that they've detected a physical tumour that wasn't there a week ago. He admits that Owen was right to ask for a scan, and says that they can remove the tumour with surgery. Katie stares at Owen in shock as she realizes she can't remember his name.
Jim takes Katie into surgery while Owen waits outside. Jack arrives and says he needs to tell them to prepare for the worse. He barges in past Owen and they discover that Katie and the entire operating team are dead. An alien life form is embedded in Katie's brain, incubated there, and emitted a poisonous gas when it threatened. Owen refuses to let Jack take Katie's brain so Jack chloroforms him. Owen wakes up in a hospital bed and demands to know where Katie is. He gets no answers and tries to tell the psychiatrist, but there's no evidence to support Owen's story. According to the report, Jim died in a car accident. The psychiatrist gives him three months of rest and Owen stalks off. He goes over the security footage but it doesn't show Jack.
Later, Owen goes to Katie's grave and sees Jack standing in the distance. He runs up to him and slugs him, accusing Jack of refusing to save Katie. Jack explains that there was nothing he could do. Owen wonders if he's having a mental breakdown but Jack assures him he's sane, and asks what Owen is going to do now. He explains that he's building something and he needs a medic. Jack points out that Owen didn't give up on Katie, and he needs someone to fight aliens. Owen insists there is no such thing as aliens so Jack takes him to the Hub and asks why he became a doctor. Owen admits that he's never been able to save enough lives, and Jack says that there he can.
Gwen finds Owen and gets him out before the windowpane drops. They've freed Tosh and get outside to discover that the SUV is gone. Jack gets a signal on his wrist unit: it's Captain John. He reveals that he has Jack's brother Gray, and then explains that he's going to destroy everything that Jack loves and treasures.