Someone has been killing the homeless of Cardiff by chewing out the backs of their necks and eating part of their brains. Gwen and Jack investigate the latest such murder, and Jack is disgusted to find that PC Jimmy Mitchell has thrown up over the gruesome crime scene. Leaving the shaken Mitchell to guard the body, Jack and Gwen visit the Casa Cali café to stake out a suspect; Toshiko has cross-referenced the murders through the Police National Database and has found that Guy Wildman, an ordinary businessman who works at the Blaidd Dwrg nuclear facility, has been taking lunch breaks that coincide with the murders. As Gwen ponders her life with Torchwood, she spots Wildman walking down the street, carrying a briefcase. Unfortunately, she knocks over her drink while standing up, attracting Wildman's attention, and he bolts. Wildman ducks into a half-finished building site, coughing up a weird pulsing organism like a starfish and spitting it at Jack to delay him. Jack stomps the thing into the ground, crushing it, and pursues Wildman up to the building's unfinished 8th floor. Wildman's shirt is caked with drying cerebrospinal fluid from his last "meal," and, realising that he's been caught and has nowhere to run, he bids Jack au revoir and deliberately falls backwards out of the unfinished building. Tosh and Owen arrive just in time to see the plummeting Wildman hit a bus, which drags his body down the street for some distance before the horrified driver can stop. The police arrive on the scene, and Gwen tries to politely brush off her old partner, PC Andy Davidson, who is irritated by her refusal to share the secrets of her new job. Owen examines what's left of Wildman's body, and tells Jack and Gwen that Wildman started to scream as he fell, as if he'd changed his mind halfway down. Jack arranges for Wildman's body to be taken to the Hub for an autopsy, and as he does so, it begins to rain.
The Torchwood team reconvenes at the Hub, where Tosh reports that she's found a cluster of similar deaths around the Caregan barracks, an army training camp in Cowbridge. Owen's initial autopsy confirms that Wildman chewed out his victims' necks and drank the meningeal fluids from their brains, but to Gwen's disgust, Owen's attitude is that the dead people were homeless and therefore unimportant. Jack and Gwen follow up a police report to find Wildman's abandoned car, and the body of his secretary, Jennifer Fallon; she apparently noticed that her boss looked ill and offered to give him a ride home, and he repaid this act of kindness by killing her and eating her brain. Jack arranges for her body to be taken back to the Hub, and while doing so, he notices a hole in his boot; it seems that the starfish creature managed to digest the boot's organic sole when Jack stomped on it. Noting that Gwen appears tired, Jack sends her back to her flat, reminding her of her promise to maintain her normal life with Rhys; nevertheless, Gwen is beginning to feel as though Rhys is part of another life that she's leaving behind her. That night, she has a nightmare about Jack drowning in a swimming pool, and wakes with a start. Rhys offers to open a window to let in some fresh air, even though it's pouring rain outside. Nevertheless, Gwen later finds out that she still has Owen's phone number, which he gave to her in a clumsy attempt to chat her up -- and despite Rhys' solicitousness, she does not throw it out.
Back at the Hub, Owen has been unwinding in a multiplayer online game called Second Reality, in which he lives another life as a barbarian warrior named Glendower Broadsword. Tosh is amused by his hobby, particularly as he hasn't realised that his avatar is female. Nevertheless, she offers to let him use the game to test her new touch-sensitive gloves and photorealistic 3-D viewing helmet. She warns him that he'll have to play a limited offline version of the game to prevent hackers from accessing the alien technology that she used to improve the experience; however, Owen soon gets bored without unpredictable live players in the mix. When he "emerges" back into the Hub, he finds that Tosh has set up holographic projectors in the R&R chamber, so that Ianto appears to have the head of a giraffe and Owen takes on Glendower Broadsword's appearance when he enters the projectors' range.
Tosh and Ianto go home for the evening, and Owen promptly disobeys Tosh's instructions and logs onto the Internet to play the full-immersion Second Reality with other players. With the help of special glasses purchased from a Mage named Candlesmith, Owen can see the true identities of the other players, and he's disappointed to learn that the nubile young Penny Pasteur is in fact Donald McGurk Jr., a 32-year-old Star Trek fan from Minneapolis. However, he gets an even bigger shock when he hits it off with a player named Egg Magnet -- and discovers, moments before she disconnects, that she is Dr Megan Tegg, the girlfriend he dumped in London six years ago. Apparently, she now works at the Cardiff Royal Hospital. Owen falls asleep at his desk and is woken by Ianto, who reacts oddly when Owen jokes that he met an online player with an interest in cybersex. Outside the Hub, the weather continues to deteriorate...
Owen completes his autopsy of Guy Wildman, and confirms that he'd been eating human brains and gestating alien organisms within his digestive system; he also finds the remains of a burnt-out alien sphere attached to Wildman's spine. Tosh reports that experimental nuclear power packs have gone missing from Blaidd Dwrg, and Ianto discovers that Wildman's body is highly radioactive. Since Owen has just spent two hours conducting an autopsy on the body, Jack confines him to the Hub with a sponge that will soak up the radiation. Jack and Gwen head for Wildman's flat to look for the stolen nuclear packs; Gwen stops Jack from kicking in the door and instead convinces one of Wildman's neighbours to buzz them in. The old lady regards them suspiciously as they head for Wildman's flat, where they surprise a blonde woman in her mid-30s who looks at Jack as though she recognises him. She identifies herself as Wildman's neighbour, Betty Jenkins, and explains that she's here to water his plants while he's on holiday.
While searching the flat, Jack enters Wildman's bathroom and is attacked by a giant starfish creature lurking in the tub. Gwen's gun has no effect on the creature, and she tells Betty to run, grabs Wildman's electric heater and throws it into the tub, electrocuting the starfish thing. Jack's shirt, coat, and skin are dissolving where the creature's suckered tentacle had a grip on him, but he assures Gwen that he will heal quickly. Since the creature is dead, he arranges for the police to place the flat under guard until Owen can conduct an autopsy. Tosh then calls to report that she's found a match for the alien device in Wildman's spinal column; another was found during the autopsy of Sgt Anthony Bee, a soldier who was recently shot dead while trying to steal military equipment from the Caregan barracks. Jack decides to investigate, but Gwen first pops back into the apartment building to ensure that Betty is safe... only to find that the real Betty Jenkins is the suspicious old lady who buzzed her and Jack in. The blonde woman has long since vanished, and Jack and Gwen thus set off for Caregan, meeting Tosh on the way.
The base commander, Lt-Colonel Daniel Yorke, is upset that Torchwood has jurisdiction over an incident that took place on his base, but he has little choice but to let them investigate. Gwen thus interviews the medical officer, Major Robert De'Ath, who admits that Sgt Bee, a popular and friendly officer, apparently killed and ate two of his own men before shooting Private Sujit Kandahal in a botched attempt to steal an amphibious vehicle. Meanwhile, Jack is enraged to find that the crime scene has already been tidied up, destroying all evidence. He investigates the contents of Bee's barracks, and finds photographs of Bee scuba diving with his friends: Guy Wildman and Sergeant Sandra Applegate, the blonde woman from the flat. Jack realises that the starfish creature had been guarding something in Wildman's flat, and that Applegate had gone there to retrieve it.
Jack, Gwen and Tosh rush back to the flat, and on the way, Jack phones Owen and tells him to find out all he can about Sandra Applegate. Gwen urges Jack to warn the police about Applegate, but he doesn't want them to interfere with his investigation -- and when they arrive, they find that the two policemen who were guarding the flat have been murdered. Sandra has returned, and in the ensuing fight, she coughs up a starfish onto Gwen's hand. Jack shoots Sandra, who falls through a window, but he then pauses to stab the starfish creature and get it off Gwen before it can do too much damage; by the time he returns to the window, there's no sign of Sandra's body. Jack returns to the bathroom and finds that the large starfish had been protecting a lead-lined box containing the stolen nuclear packs; he sets off to return them to Blaidd Dwrg, telling Gwen and Tosh to come up with a cover story to explain the policemen's deaths. However, Gwen still blames Jack for failing to warn the police of the possible danger. The weather has been deteriorating all the while, and by the time they get back to the Hub, the Oval Basin is flooded and the water level in the Hub's tidal pool is beginning to rise. Owen has finished decontaminating and apparently gone home, and Jack sends Gwen and Tosh home as well while Ianto goes to the basement, claiming that he has filing to complete. Out in the rain-soaked streets, the wounded Sandra, realising that her body has been mortally injured by the gunshot wound, remembers an old joke about the fastest way to get to hospital, and thus deliberately steps in front of an ambulance and lets it hit her.
Owen has not in fact gone home; he has instead contacted Megan Tegg through Second Reality, revealed his true identity to her, and convinced her to invite him around to her flat. There is some awkwardness between them, as Owen broke Megan's heart when he walked out on her; however, he tells her that he wants to make up for his selfishness by recruiting her to Torchwood, as her behaviour in Second Reality has convinced him that she'd be open to the possibilities of alien life. She is sceptical of his claims at first, but he wins her over by showing her a Bekaran deep-tissue scanner, an alien device that provides non-invasive images of the interior of the body. Genuinely impressed by the technology, she uses it to look under Owen's clothes, and they make love before she has to return to Cardiff Royal Hospital to start her shift. Owen accompanies her and uses the Bekaran scanner to diagnose a pregnant woman's cephalo-pelvic disproportion, proving the alien device's benefits. Megan is quick to understand the implications of its existence and the importance of Torchwood's work; although the Bekaran scanner has proven beneficial, what happens if humanity stumbles across the alien equivalent of a weapon?
Owen notices Sandra Applegate's name on the in-patient lists, recognises it and decides to investigate; however, since he's trying to impress Megan, he doesn't admit that he has no idea why Torchwood has an interest in Sandra. Dr Amit Majunath is unimpressed by Owen's Torchwood credentials, but as the storm grows worse outside, more and more patients flood the hospital and Majunath becomes too busy to stop Owen and Megan from investigating. Sandra's X-rays seem to indicate that there is a bullet lodged near her spine, but the Bekaran scanner reveals that the "bullet" is in fact an alien implant, just like the one in Wildman's body. Sandra then wakes, hears Owen explaining himself to Megan, and tells him that she needs Torchwood's help. According to Sandra, she, Tony, and Guy found an alien spacecraft on one of their diving expeditions, and were captured when they investigated. The aliens planted tracing beacons in their captives' bodies, but they were dying and were unable to prevent the humans from escaping. Sandra claims that Tony and Guy decided to wait for the aliens to die off, salvage alien technology from the ship and make their fortunes; she tried to talk them out of it but failed, and now that they're both dead, she just wants to get back to the ship and get the tracer out of her body. Still trying to impress Megan, Owen agrees to help, and Megan also agrees to come along, determined to see this weirdness through. As Owen and Megan leave to arrange Sandra's discharge, Sandra tells her young nurse, Roberta Nottingham, that she needs a quick bite to eat...
Unaware of what Sandra has just done, Owen and Megan drive her out to the Wetlands Reserve, where the alien ship's escape pod is hidden. Although Sandra appears to be growing weaker from her gunshot injury, she insists upon returning to the ship, telling Owen that the typhoon swamping Cardiff is a result of the ship forcing its way through the Rift. Owen hadn't intended to expose Megan to so much so quickly, but he nevertheless allows her to accompany him and Sandra down into the Bay. Inside the alien ship's control room, Sandra points out two control frames that she claims will enable Owen and Megan to reverse the ship's engines and send it back through the Rift -- but once they have strapped themselves in, the frames plant control spheres in their spines, and the entity controlling Sandra's body vacates it and moves into Megan's. Owen watches helplessly as Megan activates a control to reveal an alien life form sitting in a nearby cabinet; this is the true body of the ship's only survivor, a Bruydac warrior. Sandra, Guy and Tony Bee did indeed stumble across the ship as Sandra had claimed, but the spheres in their bodies were control units, not trackers. The Bruydac's consciousness has been moving from host to host, trying to find more fuel for its damaged ship. The act of possession burns up human cerebrospinal fluid at an accelerated rate, which is why the Bruydac's hosts had to feed on others to replenish their own. The Bruydac informs the stricken Owen that Megan never stopped loving him, which is why she went along with all of this craziness. Owen begs it to use his body instead of hers, but it leaves him connected to the control frame and leaves to complete its task, after using Megan's body to cough up another starfish onto the dazed and dying Sandra Applegate.
Back at Torchwood, Jack receives a politely frantic phone call from Jonathan Meadows at Blaidd Dwrg, and learns that there are still two nuclear packs missing. Tosh then reports that her weather analysis indicates that something is emerging from the Rift beneath the Bay, causing a localised typhoon that is going to get worse until the source of the disturbance is removed. Jack orders Tosh and Gwen to find Owen and investigate the disturbance under the Bay, using the Torchwood mini-sub; he himself returns to Wildman's flat, hoping to find the two remaining nuclear packs. They aren't there, but Tosh finds that the last person to call Owen's cell phone was Dr Megan Tegg of Cardiff Royal Hospital. Jack goes to the hospital, where he learns that young nurse Bobbi Nottingham was recently murdered, the back of her neck chewed out. The Bekaran scanner is lying near Bobbi's body, as Owen forgot to pick it back up after using it to "diagnose" Sandra Applegate, but Owen, Megan, and Sandra have long since gone.
On his way out of the hospital, Jack notices a salesman carrying a briefcase, and realises that Wildman's briefcase disappeared at some point during their chase. Jack rushes back to the building site where Wildman died, but the driving rain has become even worse, and he accidentally hits and kills a Weevil in the SUV. He is forced to stop and load its body into the SUV, and by the time he gets to the building site, there's a Mini parked outside, its owner lying dead in the driver's seat with the back of her neck chewed out. Jack rushes back up to the eighth floor to find that Megan Tegg has found and retrieved Wildman's briefcase. When she quotes something that Wildman had said in the same circumstances, Jack realises that the true enemy is moving from body to body, using and discarding human lives as interchangeable tools. It insists that it just wants to escape, but when he refuses to let it get away with murder, it pulls the two remaining nuclear packs out of the briefcase and threatens to smash them together, causing a small atomic explosion that will scatter radioactive fragments across the entire city; however, the alien will survive the explosion by moving out of Megan's body and into another to continue its search for fuel elsewhere. Before it can smash the two rods together, Jack shoots Megan in the forehead, killing her.
Gwen and Tosh have descended into the Bay and found the alien ship. Owen is unconscious in the control frame, and the starfish has eaten off the dead Sandra Applegate's face. Gwen insists upon taking Sandra's body back to the Hub along with Owen. When Jack kills Megan, Owen revives and attacks Gwen, trying to chew out the back of her neck; fortunately, Ianto arrives just in time and Owen is forced to flee into the depths of the Hub. Jack calls the Hub, learns what's happened, and orders Ianto to restrain Owen and kill him if necessary. While Ianto and Tosh search the Hub for Owen, Jack orders Gwen to fetch some scuba gear and the harpoon gun, and together, they return to the ship by diving down through the tidal pool. When they arrive, Jack sets the engines in reverse; the ship will tear itself apart backing through the Rift, but the Rift itself, and thus the weather, will return to normal. Despite Gwen's protests, Jack then cold-bloodedly executes the Bruydac by shooting its body with the harpoon gun, claiming that it's forfeited its right to survive by callously using other lives as tools. He then tells Gwen his plan to dispose of the Bruydac's consciousness, and despite her reservations, she stands back and does nothing while he connects himself to the control frame and allows it to implant a sphere in his spine.
Ianto and Tosh trace Owen's mobile phone to the cells, where they find that he's planted it on the captive Weevil. Ianto zaps the Weevil, stunning it with a device that he claims was recovered from the wreckage of Torchwood One. Tosh then comes up with a plan to lure Owen into a trap, and returns to the Hub. Owen is now desperate to feed, and as he approaches Tosh, Gwen calls the Hub and, apparently panic-stricken, tells Tosh that Jack has had a control sphere implanted in him. Owen attacks Tosh, but she has repositioned the holographic generators, and he finds himself attacking her Second Reality avatar while her real self hides in the boardroom. He is thus caught off-guard and easily overpowered by Ianto, who was hiding underwater in the tidal basin. Ianto injects Owen with a powerful sedative, but the Bruydac has overheard Gwen's frantic call and thus moves out of Owen's body and into Jack's, burning out the control sphere in Owen's body as it goes. However, when it opens Jack's eyes, it finds that Gwen has restrained Jack's body in the cage where its original alien body had been resting. Following Jack's earlier instructions, Gwen dons her scuba gear and opens the ship's airlocks, and the creature, having run out of hosts, finds itself trapped in Jack's body as the ship fills with water. Unlike its human hosts, it has no belief in an afterlife, and when Jack drowns, the creature has no other life to pass on to.
Gwen takes Jack's body back to the Hub, where he revives despite having gone without air for several minutes. Unaware that Jack cannot die, the others assume that the Bruydac panicked and incorrectly assumed that he was dead. The typhoon is dying away, and as Cardiff slowly returns to normal, Jack takes his team out to Casa Celi for dinner. Privately, he assures Owen that he was picked for Torchwood because he's the best, and that there's no need for him to prove it to anyone. Owen nevertheless feels that Megan died because of him -- and when the team spots a Weevil running past on the street, Owen is the first out of the door in pursuit.