Less than a day after the death of Sir Giles Walbridge, the head of the Environmental Agency's Species Recovery Program, three Agency employees and their pilot are killed in a helicopter crash just north of Merthyr Tydfil. Jack is horrified to learn that one of the victims is Walbridge's personal assistant, 27-year-old Alice Proctor, the daughter of a friend. Jack heads out to do some footwork while the others investigate the crash from the Hub, but they work through the night and turn up no leads; all they know is that the victims were returning from an archaeological dig in Newton.
The team takes a break from their work to go for breakfast at a local café, but there, they see a news report on the death of billionaire philanthropist Sir Robert Craig -- which features a stock photo of Craig standing next to Sir Giles Walbridge. They return to the Hub to resume work, but Ianto begins to get worried about Jack, who hasn't yet reported back. Gwen contacts an old friend in the police, and learns that Jack's phone number was found in Alice Proctor's purse. Unable to contact Jack's mobile, Tosh brings up its call records, and learns that he made three calls last night: two to Robert Craig, and one to a fertility clinic in Caerphilly. He also received a return call from the CARU Clinic, and he received a call from the dig in Newton less than 20 minutes before the helicopter crash. Unable to reach Jack and unable to find any clues in his office, Gwen decides to visit the dig with Owen while Ianto visits the CARU Clinic and Tosh co-ordinates the investigation from the Hub. When Ianto arrives at the clinic, however, he catches a glimpse of a black-clad figure running away, and finds that the three women who run the clinic have been savagely murdered.
Owen and Gwen arrive at Newton House, where they meet archaeologist Steven Parks. Parks is quick to realise that the Torchwood operatives believe that his colleagues were murdered, but Gwen calms the shaken man down by asking him about his dig. He explains that geophysical scans have revealed a hidden crypt buried beneath the historic building, and evidence suggests that it could be the last resting place of the famous Welsh philosopher Thomas Vaughan. Vaughan was vilified by his peers for his work, which he published under the name Eugenius Philalethes, but the subjects he studied are commonplace in today's hospitals and universities. The chapel contains pagan statues and icons of Hermeticism alongside Christian iconography about the resurrection, and Parks explains to the openly sceptical Owen that alchemy is about more than turning lead to gold; it's about transmogrification, both chemical and spiritual. Vaughan was studying the transition of the soul and the conquest of death, and Parks thus feels it's appropriate that the sarcophagus contained not a physical body but three canisters of ancient, rotted vellum, which have been sent back to Cardiff for reconstruction. The archaeologists didn't find Vaughan's body, they found his unpublished alchemical studies -- his legacy, or his soul.
Jack has spent the last eleven hours in a police interrogation room. DC Kate Jenkins, the good cop, brings him tea and tries to establish a rapport with him, but Jack knows how this works and waits out her routine until her DCI arrives. The interrogator gets straight to business: within the last 24 hours, Robert Craig, Alice Proctor, and Megan Brook of the CARU Clinic have all been murdered -- and have all had contact with Jack. The DCI is convinced that Jack is responsible for the murders and believes himself to be above the law, but he warns Jack that forensics will prove Jack was in the car with Craig at the time of the crash. Jack promises to explain everything once he's been given his one phone call, and the interrogator eventually gives Jack five minutes alone with a mobile. Jack calls Tosh in the Hub, but chooses his words carefully while explaining what's happened, aware that his side of the call is being monitored. Tosh reads between the lines and realises that Jack is subtly informing her that the CARU Clinic holds the key to the mystery.
On the way back from Caerphilly, Ianto realises that he's being followed by a black Honda sedan. He tries to shake it off by turning onto the deserted hillside roads outside Cardiff, but realises his mistake when the sedan speeds up and tries to run him off the road. He calls Tosh for help, and Tosh contacts the police and tries to direct Ianto to safety. However, the route to the intersection where the police are waiting takes Ianto onto a rough road with only a thin metal barrier protecting him from a sheer drop -- and the Honda sideswipes him, knocking his car through the barrier. Ianto manages to leap out of the car as it goes over the edge, and although he's badly injured doing so, he still manages to hide himself beneath the overhang. The driver of the black Honda stops and emerges to watch Ianto's car tumble down the hill, crash, and burst into flames on the valley floor. The Honda then leaves, and once he's alone, Ianto tosses shale down the hill, eventually attracting the attention of the police gathered around the wreck of his car. He then concentrates on not passing out while they arrange to rescue him.
Tosh contacts Gwen and Owen as they return from Newton, and tells them that Jack has been arrested on suspicion of murder and that she's lost contact with Ianto. Gwen calms down the worried Tosh, telling her to find out which laboratory is examining the parchments from the archaeological dig. She and Owen head to the scene of the crash, where they find that Ianto is alive and surrounded by emergency services; however, he's lost a lot of blood and a piece of shale is embedded dangerously close to his spine. A Mountain Rescue helicopter flies Ianto off to hospital, and Owen keeps Gwen from losing control as she vows to find out what's happening and who's trying to kill her friends. Tosh then reports that the laboratory holding the parchments reported a break-in last night; unsurprisingly, the parchments were the only artefacts that were stolen. Frustrated that their unknown enemies are always one step ahead of them, Gwen points out that Robert Craig is the odd man out; everyone else has been killed before Torchwood got on the scene, but Craig was only killed after Jack contacted him. What did Jack know about him, and what is his connection to the CARU Clinic?
Back in the Hub, Tosh hacks into CrimNet and arranges for the CARU Clinic's hard drives to be sent to the Hub instead of Cardiff CID. While waiting for them to arrive, she researches the life of Thomas Vaughan and prints out the portrait from his biography. One source suggests that he was poisoned by mercury fumes during his alchemical experiments, and another claims that he died drinking a concoction that he believed would grant him eternal life. He was once placed on trial for consorting with the Devil, and 200 years after his death, a woman named Diana Vaughan claimed to possess papers proving that her ancestor had founded a Satanic society called the Arcanis Servitorus -- the "Silent Watchers" or "Hidden Saviours," depending upon the translation. It doesn't help her current investigation, but it makes for good reading.
Gwen and Owen visit the university's biochemical research facility, where the Newton documents had been sent for study. The facility has elaborate security measures in place, including fingerprint scanners, and Gwen and Owen must wait for the night watchman, Raymond, to print up visitors' passes before they can speak to Ella Contas, the scientist in charge of reconstructing the Newton documents. Dr Contas takes Gwen and Owen up to the archival storage area, where she shows them that the thieves failed to steal the digital reproductions of the documents. The amount of reconstruction work she can do is limited without the originals, but she's seen enough to confirm that the Newton Codices contained many secrets hidden behind elaborate ciphers and extra levels of obfuscation. Loosely translated, some of the hidden messages imply that Vaughan was looking for the Philosopher's Stone, and that he sought to create an immaculate child conceived without conception -- a religious miracle in his time, but relatively commonplace these days thanks to discoveries in genetic engineering and cloning.
Dr Contas takes Gwen and Owen back to her office to continue their discussion. Owen automatically gives the room a once-over, and sees a bank of security monitors, on which he can see Raymond's body lying in a pool of blood by the elevators. Before he can warn the others, somebody shoots Dr Contas in the head. Owen and Gwen take cover, and Gwen shoots their attacker as he enters the room to finish them off. The dead man has a military buzz cut and a tattoo that resembles the markings in the crypt at Newton House. Owen contacts Tosh and has her hack into the facility's fingerprint scanners, and she discovers that two more "visitors" logged into the building but have yet to log out. Furthermore, they've been there all day; the digital photos were left here deliberately as a lure, and the killers have been waiting for someone to come asking about them. Tosh is also able to identify the dead man as Christian Vancarlo, a former soldier who was dishonourably discharged after a scandal in Darfur; he subsequently found employment with Azureus Security, a front company owned by Robert Craig. Owen takes the dead man's gun, and he and Gwen get out of the building and down to the SUV, evading two men who attempt to gun them down as they flee.
Jack's interrogator returns with damning new evidence: Robert Craig's fatal crash was photographed by a speed camera, and the still images clearly show the car crashing into a tree and bursting into flames -- and Jack Harkness stumbling away from the wreck without a mark on him. There are no skid marks, which implies that the car was crashed deliberately, and the photos seem to show Jack standing guard over the car as it burned to ensure that Craig didn't get out. Jack points out that the photos don't convey the immediacy of the event, the smell of burning petrol, or the sound of the engine ticking, which he claims caused him to panic and freeze once he was out of the car. Also, he knows why he hasn't been formally charged yet: Robert Craig drove an imported car with the driver's seat on the left-hand side, which means that it was Craig, not Jack, who was driving the car when it crashed.
Tosh picks up the CARU Clinic's hard drives from a courier at the information kiosk, but finds that the killer has already been through them with a shredder. While the Hub's computers trawl through the digital wreckage, trying to reconstruct the data, Tosh researches Robert Craig's past, hoping to get some idea of what she's looking for. She quickly turns up several discrepancies: Robert Craig's parents both died on the same day in an accident, and hidden records indicate their only son died at birth. Craig's educational background also appears to have been forged, and although Tosh finds a photograph of Craig crouching beside a young boy who resembles him, there is no other indication anywhere else that he has a son. Gwen and Owen then return, shaken by their close escape, and Owen takes a look at Tosh's research and immediately spots what she'd been too close to see: the photographs of Robert Craig are identical to the woodcut of Thomas Vaughan.
The reconstructed data from the CARU Clinic reveals that its fertility services were a front for a research project to map the human genome, repair genetic damage, and engineer human embryos to order. The genetic coding mapped out in the files could give the human body the ability to repair genetic damage on its own, basically granting immortality. Robert Craig's records from the clinic indicate that he's sterile, and the fact that he looks exactly like a man who was researching immortality centuries ago can't be a coincidence. Robert Craig is Thomas Vaughan, his son Simon is in fact his clone, and his private army, the Arcanis Servitorus, has been killing everyone who knows his secret. Jack really did kill Robert Craig to avenge Alice Proctor's murder, but now that his friends know the truth, they can get him out of trouble by stealing Craig's body from the morgue.
The DCI's attempt to pin the murders on Jack comes to nothing when DC Kate Jenkins returns with bad news: Craig's body has vanished, and the DCI's signature is on the release papers. He denies doing this, but now he has no evidence against Jack apart from a set of photographs that could easily have been faked -- and Jack has solid evidence that the man he's accused of killing, Robert Craig, died on the day he was born, 17 April 1956. The DCI is forced to release Jack, who joins the rest of his team and visits a rugby field where a man with a military haircut is watching young Simon Craig play. Jack confirms his friends' deductions, but reveals that the cloning process was flawed and that Simon Craig's body is already suffering from the effects of genetic damage. Alice Proctor discovered the truth about Thomas Vaughan, but she told Sir Giles before she told Jack, and Sir Giles signed everybody's death warrants when he attempted to blackmail Craig. Jack has avenged their deaths, and since Simon Craig is his own person, he isn't doomed to repeat his father's crimes; in any case, he is sterile, will probably die in his 20s, and is guarded by a ruthless private army. Jack thus decides to leave matters where they lie, and visits Ianto in hospital to assure him that it's over.