In Kentucky, killer Oswald Danes awaits execution as a few protestors gather outside. A former school teenager, Danes defended himself for killing a 12-year-old-girl by telling the police, “She should have run faster.”
The prison officials administer Danes’ lethal injection while the girl’s mother Joan watches from the gallery. Danes has nothing to say and the execution begins. The killer convulses in pain and pulls the arm of the table free. However, he doesn’t die and the guards rush in.
Rex Matheson is driving when Esther Drummond, his friend and fellow agent at the CIA, asks if he’s heard of Torchwood. Someone has mailed an email with the single word, “Torchwood,” to every CIA head on the U.S. East Coast. All the CIA has been able to determine is that the Torchwood Institute is part of the UK government. The email file wipes itself out, and Rex tells them to pass Torchwood onto someone else. The truck ahead of him suddenly brakes and the pipes in the back go shooting back, impaling Rex... who doesn’t die.
Gwen Cooper wakes up and tells her husband Rhys that she’s had a bad dream... about Torchwood.
Dr. Vera Juarez tends to Rex and Esther accompanies her into the ER. The doctor explains that Rex is their second DOA that the hospital is overwhelmed with “patients”: people who can’t die.
The next day, Gwen and Rhys are tending their yard when a tourist helicopter flies over. Gwen looks at it nervously and then goes in to feed their baby, Anwen. As she tells her baby a story about one of her encounters in Torchwood, Rhys tells her to stop. There’s a knock at the door and Gwen and Rhys go for their arsenal of guns. They open the door and find hikers there asking for directions. Gwen tells them that she’s busy and shuts the door, and then watches from the window as they go. She worries that she could have shot them, but Rhys says that they’re safe and no one knows that they are there.
As they go down the road, the hikers look briefly at each other and continue.
In Washington, Dr. Juarez sees Esther in the waiting room. She informs Esther that three station chiefs have been to see Juarez, and that she’s told them that Rex is fine. Esther thanks her, and Juarez explains that it’s not only Rex, but everyone else who should have died last 24 hours. No one has passed away at the hospital, and Juarez has confirmed with other hospitals that no one else has died anywhere in the last 24 hours.
The news reports continue as the “miracle” becomes common knowledge. Thirty-six hours, and nobody has died since what the media has dubbed “Miracle Day.”
Alexander Peterssen of the Kentucky Governor’s Office comes to prison see Danes and offers the Governor’s condolences and apology. Danes wonders when they will release him, and Peterssen notes that they can’t release him just because the execution went amiss. The convicted murderer says that his lawyers differ and that sentence was carried out. He quotes the U.S. Constitution and points out that he has already paid his price. Peterssen hesitates and Danes promises that if he isn’t released, he will sue the Governor directly for wrongful imprisonment.
Esther receives word from her superior, Charlotte Willis, that their station chief, Brian Friedken, has shut down the investigation into Torchwood. When she checks with another agent, Noah Vickers, Esther confirms that Friedken has collected all files on Torchwood, and according to what they did have, everyone associated with Torchwood died young and in action.
The pundits continue to discuss the impact of what has happened and how it started. Rex watches the news and breaks into tears. Juarez arrives and explains his “condition,” and he wonders if he will get better or his injuries will continue. The doctor tells him that he’s lucky and that they have time to fix him.
In Wales, Rhys and Gwen are painting their house when the phone rings. Sgt. Davison, PC Andy, calls to give her a coded message that her father is in the hospital at Cardiff. Gwen tells Rhys that they have to go back.
Esther goes to the CIA archives to find any Torchwood files that Friedken’s people may have left behind. She finally files a heavily redmarked file referring to box 456. The box contains clippings on various paranormal phenomena in England and photos of Captain Jack Harkness from 1939. Esther looks up and sees a man move from the shadows: Jack Harkness. He asks her to come with him, and Esther runs off. She gets to the desk and finds the receptionist, dead. Jack comes up behind her and tells her to get down, and then shoots a commando preparing to shoot her. Captain Jack shoots the commando down but discovers that he has explosives on him. The commando triggers the explosives, and Jack grabs Esther and gets her out just in time, diving out the window into the fountain below.
As the fire trucks arrive, Jack offers Esther a bottle of water and explains that the killer was after him. Esther explains that she was talking to her friend about Torchwood when Rex crashed, and she blames herself. She asks him how there could be a photo of him from 1939 and Jack claims that it was his father. He then clutches at his arm, surprised that he appears to be hurt. Jack then tells Esther that the British government set up the Torchwood Institute in the late 19th century to investigate strange phenomena. Esther asks him about the photo of Gwen and Jack explains that she’s still alive and the last one left. To keep Gwen safe, he plans to make sure that Torchwood remains dead and buried. Someone else released the email, and Jack released a malware virus to erase any trace of Torchwood. He also tells her about Retcon: an amnesia drug. Esther realizes that he has drugged her as she passes out.
Rex calls Juarez, who tells him to check Ringmain. Jack arrives, posing as an FBI agent, and asks to see her. Meanwhile, Rex asks an orderly what Ringmain is, and he explains that it’s the internal security system. After making a call to the CIA, Rex ties into the internal cameras and watches as Jack and Juarez meet with a coroner, Dr. Santini. They have recovered the body of the killer from the archive building and confirmed that he is still alive even though his body has been all but destroyed. Jack asks what might happen if they detach the head. Juarez objects but the coroner cuts through the neck. The head remains alive and the coroner suggests that whatever is responsible is not of Earth.
Gwen and Rhys arrive at the hospital and Andy greets them. He explains that Gwen’s father had two heart attacks but is now stable and out of ICU. People have gathered at the hospital and Andy explains that people are worshipping doctors since Miracle Day, 48 hours ago. He brings them up to speed on what has happened as they go to Geraint’s room. Her mother Mary is there and complains that they came out of hiding, but is happy to see her granddaughter. Gwen talks to Geraint, who wonders if he should be dead. Her parents ask if she knows anything, and Gwen says that Torchwood used to handle such things but now she’s the only one left.
Jack goes to the abandoned apartment building where he lives and reads Internet articles on Miracle Day. At the hospital, Andy and Gwen go over the same articles, which talk about how some nations have stepped their wars and others are eager to continue. Only humans are affected. Andy points out an article noting that 300,000 people normally die per day, and 500,000 people are born every day. Miracle Day has caused the greatest population boom in history and in four months society will collapse due to lack of food.
Rhys comes out and complains that Gwen is investigating things when she promised not to. In response, she shows Rhys that there is already an overflow of patients. Rhys insists that she can’t dare get involved again. He warns her that people will also think that it’s Torchwood-related, men with guns will come for her. Now they have a daughter and Gwen can’t put her in danger. When she worries about her father, Rhys points out that he’s not going to die and Anwen could live forever. He wonders if they should let it happen and Gwen agrees to go home.
Esther wakes up at home with no memory of the previous night. She finds the bruise caused by the fall into the fountain but doesn’t know where it came from.
Jack examines himself in the mirror and finds bruises on his side.
Esther arrives at work and Noah gets her the last remaining file on Torchwood. She thumbs through it and finds a photo of Gwen and then puts the file away. Rex calls her and asks what the CIA’s progress is. The discussion turns to Torchwood and they realize that the email transmission came through just as Miracle Day began. As Rex gets dressed, he tells Esther that there must be a connection between Miracle Day and Torchwood. He gets Esther to tell him what they have on Torchwood and she admits that she doesn’t have much. Rex gets outside and hails a taxi, while telling Esther to book him a flight to UK and prepare a Requisition 15 to take a handgun on a flight. The requisition is refused and he tells Esther to get him a gun from their British division.
As Rex boards the plane, Esther returns home and he tells her to find out everything she can about Gwen Cooper using his password to access the system. He starts to give it to Esther, but the passenger next to him takes away his phone as the plane lifts off. When Rex arrives in Wales, he calls Esther and gives her his password, and she turns up Gwen’s connection to Andy, her liaison. He made a call to a phone number on the witness protection plan. Esther sends him the coordinates of the house in Wales and Rex arrives at the Cooper home. He hobbles in and finds Gwen with a gun. Rex identifies himself and then collapses.
The news announces that Danes’ survival has been declared an act of God, and the state now has the burden to prove otherwise. Danes is released and is driven out through the gate, where hundreds of angry protestors yell at him.
Rhys ties Rex to a radiator and tells him that they’re leaving. Rex easily frees himself before Gwen and Rhys can leave. Rex explains what happened to him and demands to know what it has to do with Torchwood. A helicopter arrives outside and a man fires a rocket into the house. It goes through the windows and out the back and Gwen fires back, killing the shooter. As the helicopter retreats momentarily, Gwen, Rhys and Rex run to the car. The helicopter returns and opens fire, but Jack arrives to fire at it and forces it to back off, Rex realizes that Jack was on the plane next to him during the flight.
The quartet drives down the beach in Jack’s Jeep. Jack has left a gun in the back and Rex returns fire at the helicopter as it pursues them. As Jack brakes to a stop, Gwen fires a rocket launcher at it, bringing it down. Gwen and Jack look at each other and smile as they observe the wreckage.
In Cardiff that night, Gwen notifies her parents that they need to pick up Anwen. Rhys complains that his wife is rejoining Torchwood. Jack reveals that he has a cut on his arm and that he’s been transformed back into human. The Cardiff police arrive and surround Jack, Rhys, and Gwen, and they realize that Rex has set them up. Andy is there and tells them that he has no choice, and Rex tells them that he’s conducting a Rendition and extraditing them to the U.S.