Deep in the tunnels at CERN, a technician named Leon Foiret is inspecting the coolant pipes for the Large Hadron Collider when a ghostly voice begins whispering to him from thin air. There's nowhere for him to run as the voices close in on him...
In Cardiff, Jack leaves Gwen and Ianto to chase a Weevil through the Bay area while he takes a phone call from Martha Jones. UNIT is providing security for the launch of the LHC, but people have begun to disappear from the complex, including an old friend of Martha's. Jack, Gwen, and Ianto head to Switzerland to investigate undercover, and on the way, Jack explains that the LHC is a gigantic particle collider with which the scientists at CERN intend to break apart matter into fundamental particles. If the experiments succeed, they may even identify the theoretical Higgs particle, the most fundamental unit of existence. However, some believe that the experiments could have disastrous side effects on space and time. Perhaps the people who disappeared are being removed because they found out something they shouldn't...
Martha greets the team upon their arrival in Switzerland, and explains that her friend Julia Swales works at CERN as a medical doctor. Patients began turning up with odd symptoms, and were supposedly sent on to a specialist in France -- but Julia discovered that they hadn't turned up at their destination, and then she too disappeared. UNIT has found no real evidence of wrongdoing and is too busy dealing with standard security to investigate properly, which is why Martha has invited her friends from Torchwood to investigate. She provides them with fake IDs identifying Ianto as the Welsh ambassador, Gwen as his wife, and Jack as their personal assistant, and takes them down into the underground city of research offices and laboratories. There, they meet Professor Katrina Johnson, head of the LHC project; she's worked towards this launch all of her life, and is eagerly anticipating the things that the LHC can teach humanity about the secrets of the universe.
Instead of taking the Torchwood operatives to the viewing area, Martha takes them to the sickbay. Her boss, Dr Oliver Harrington, is just leaving to observe the launch; Jack notes that Harrington has sad eyes, and Martha admits that he hasn't fully recovered from the death of his wife last year. Gwen examines Leon's body using the Bekaran deep-tissue scanner, and to everyone's surprise, Leon's body begins to glow. Jack sends Gwen and Ianto to look into the patients' backgrounds while he scans Leon with his vortex manipulator. While they're alone, Martha asks Jack how he's coping with Tosh and Owen's deaths, as she can tell that he blames himself and is concentrating on his work to ignore his grief. Jack's analysis then reveals that Leon's body is glowing because it's disintegrating; something has removed all of the neutrons in his body, and Jack realises that he knows what it is.
Gwen and Martha determine that all of the patients had fallen ill in the LHC's maintenance tunnels, and that the LHC went through a test run back in May. Jack believes that the test created a dimensional bridge that an alien entity slipped through; he once saw a creature like this destroy an entire human colony in the future. Torchwood must neutralise the creature, prevent the big launch from bringing through more of its kind, locate the missing patients, and discover who arranged for them to disappear. Satellite pictures reveal a small building on the surface that doesn't appear on the site plans, and Martha goes to investigate while Jack tries to stop the launch and Gwen and Ianto hunt for the alien in the maintenance tunnels.
Gwen and Ianto circle the tunnel on small bicycles, and Ianto takes a childlike glee in the discovery that his bicycle has a little bell. Martha speaks with Gwen over their radio headsets, and Gwen admits that she's not coping with Owen and Tosh's deaths very well. Martha then arrives at her destination, and discovers that her friend Julia and the other missing patients are all hidden inside the maintenance building -- and they're all comatose and glowing like angels. Meanwhile, Ianto hears a voice calling out to him from the dark, calling him "coffee boy" and claiming to be Owen. The dead are lost in the darkness, and they're hungry...
Jack bursts into the control room, identifies himself as Torchwood and orders Johnson to shut down the launch. Johnson scoffs at his claim that the test run summoned an alien entity that feeds on the neutrons in the human body, but Gwen then reports that Ianto has been attacked, and Martha reports her discovery. Someone in a position of authority must have hidden the patients away and faked their medical records to ensure that nothing interfered with the big launch, but the bewildered Johnson insists that she has no idea what Martha is talking about -- and even if she believed what she's hearing, it's too late to stop the activation process now. While Jack tries to convince Johnson that something terrible is on its way, Martha tries to do what she can for the glowing patients -- until Dr Harrington arrives and pulls a gun on her, threatening to shoot her if she interferes further.
Johnson is beginning to accept that something odd is going on, and when she agrees to lock down the facility, Jack explains how to prevent another breach. Before they can put his plan into action, however, Harrington arrives, holding Martha at gunpoint and insisting that the launch continue. He claims that it doesn't matter if even if he does kill Martha, because he knows that there's an afterlife; after the test run in May, he heard his dead wife speaking to him, and became convinced that the LHC had opened a gateway to Heaven. Jack and Martha try to explain that he's being misled by monsters that will devour the entire population of Earth if the launch goes through as planned, but Harrington refuses to listen and runs down into the tunnels to ensure that the launch succeeds. Martha follows him, while Jack and Johnson remain in the control room to reverse the polarity of one of the LHC beams before Harrington can lock down the system. Instead of two beams of protons, the LHC will smash a beam of protons into a beam of anti-protons; the two beams will cancel each other out, closing the portal, and creating the Higgs particle as a side effect.
Ianto tries to resist the siren call of the creature, but deep down, he wants to believe that there's more to death than just death. The creature then takes on Lisa's voice, and by the time Gwen finds Ianto, he's started to glow. As Gwen tries to carry him out of the tunnels, Ianto begs her to let him go, sobbing that he wants his lost friends and loved ones back again. Gwen resists the creature's call and manages to get Ianto the tunnel exit, where she runs into Harrington. Harrington helps her to get Ianto out of the tunnel, but then leaps through the door as Martha arrives and seals himself in the tunnel. There, he calls out to his late wife, but the creature sneers at him, as it has what it wants and doesn't need him any more. The horrified Harrington realises that Jack was right all along, but as the LHC powers up, he finds some last shred of dignity and stands up to the creature, telling it that humanity is stronger than it thinks. The particle collider then activates, and both Harrington and the creature are killed when the proton beam meets the anti-proton beam. Up in the control room, the screens display the Higgs particle for all to see, and Johnson stares in awe at what Jack has already seen: the fundamental unit of life and existence.
Ianto and the coma patients begin to return to normal once the creature has been destroyed. Johnson thanks Jack for all that he's done, and Martha promises to report on Harrington's fate to UNIT. As Jack, Ianto, and Gwen prepare to return home, Ianto quotes Tennyson on the nature of death, and wonders with Gwen why Jack never tells them what he knows about the future. All Jack will say is that for humans, the act of asking the questions is enough, even when they don't get answers.