Clumsy but well-intentioned GP Bob Strong is having trouble with one of his patients, Saskia Harden. She has been sent to him for psychiatric counselling after trying to drown herself several times, but she doesn't seem depressed at all; in fact, something about her attitude frightens him. When she attends her session, she is wearing a long raincoat and apparently nothing else underneath it, and she looks him straight in the eye and tells him that she needs a man to help her procreate. Strong hangs onto his professionalism and explains that he's not permitted to fraternise with patients, and somehow feels when she leaves that he's had a narrow escape. Nevertheless, he asks his colleague Ieuan Davis for advice, and Ieuan advises him to go for it; perhaps a proper relationship will be just what she needs to rein in her suicidal tendencies. Strong decides to give it a shot, but the receptionist, Letitia Bird, tells him that Saskia hasn't provided them with her phone number, and the address on file is nonsensically located out in the middle of the Marshlands. In any case, Strong seems to be coming down with the same sore throat that is affecting many patients at the clinic.
Jack and Owen are hunting a giant Weevil, nicknamed "Big Guy," through the abandoned Evans Fish Emporium, site of a recent discharge of chronon energy from the Rift. The night watchman was found eviscerated two nights ago, and Jack and Owen assume that Big Guy is responsible -- until they find Big Guy's disembowelled corpse and are attacked by an indistinct figure that bursts up out of a stagnant pool of water and flees. Jack and Owen take Big Guy's body back to the Hub, and on the way, Owen complains that he's coming down with a cold. Back at the Hub, Ianto reports that he's cross-referenced recent chronon discharges to police reports, and has come up with something strange: a woman named Saskia Harden has been repeatedly pulled out of local canals and pools after apparently trying to drown herself. The police have so far failed to notice that Saskia has no official identity on file, apart from her records at the Trynsel Medical Centre. Owen visits the centre to speak to Saskia's doctor, and while there, he notices that several patients have sore throats and that one woman has started to cough up blood. Dr Strong has gone home sick, and when Owen visits him at home, he realises that Strong is quite seriously ill. Putting aside the question of Saskia Harden for the moment, Owen takes a blood sample, telling Strong that he's a government official investigating a possible pandemic.
Gwen and Tosh have gone out to the Marshlands to investigate more chronon discharges, which Tosh hopes are natural fluctuations caused as the Rift settles down from the time shift to 1918. They stop at a service station for coffee, and meet a grubby old man who identifies himself as Professor Leonard Morgan, an old friend of Jack's. Len leads them to Greendown Moss, but warns them not to set foot on it; it's a floating bog, a thick layer of peat moss over open water, and one wrong step could cause them to sink without trace. Also, the bog is allegedly haunted by a water hag named Sally Blackteeth who lures men to their deaths -- or worse. Gwen and Tosh walk out onto the bog, scanning for chronon energy, but Tosh steps off the safe path when she sees something moving and begins to sink. Professor Len follows Gwen out onto the moss and helps to pull Tosh back to safety, but the disturbance churns up the peat and reveals a desiccated human body. Tosh discovers that the body is saturated with chronon energy and decides to take it back to the Hub. Professor Len stays out on the bog, and once Gwen and Tosh have gone, Sally Blackteeth appears before him. He's known for some time that she is real, and he only brought Gwen and Tosh out to the bog because he owed Jack a favour. He warns Sally that she's made a mistake in taunting them by returning the corpse, but Sally Blackteeth laughs and slashes Len's throat open with her talon-like fingernails.
Back at the Hub, Jack is dealing with UN red tape and writs from the Hokrala Corporation, and isn't interested in Owen's report on Bob Strong's illness -- at least not until the blood tests reveal that Strong has no infections and the NHS database indicates a spike in local respiratory complaints over the past few weeks. Jack concedes that the matter is of interest, but orders Owen to prioritise conducting an autopsy on the corpse from the swamp. As Owen begins to cut into the body, however, the decades-old corpse sits up and grabs Gwen by the throat, gurgling at her as if screaming. Jack shoots it in the head until it stops moving, and the shaken operatives restrain the corpse in case it comes back to life again. Tosh reviews the footage of the attack, and when she enhances the audio, she discovers that the corpse was saying "Water hag." Perhaps it saw Gwen's long floating hair and mistook her for the thing that killed it.
The corpse begins to twitch again, and this time, a shape like a baby made out of mucous tears its way out through the body's throat and jaw. Owen freaks out and shoots the creature repeatedly, claiming to have felt an instinctive repulsion to it. Tosh manages to piece bits of the creature's body back together, and determines that it was a homunculus composed of mucous, mud, and some vegetable and animal matter. Gwen researches water hags on the internet and finds that they're clumps of moss that resemble old women lurking underwater; the mythical version is that they're witch monsters who lure unwary travellers to their deaths, and who make children out of mud and mucous. More significantly, there have been nine sightings of water hags around the Rift within the past year. Ianto points out that there may be a connection to the mysterious Saskia Harden, who has always been found submerged in stagnant pools but may not have been trying to drown herself after all.
Bob Strong has called in sick, but hasn't told Ieuan about the visit from Owen, as he doesn't want to start a panic. Strong's mother calls him to ask if he'll be visiting for his father's 80th birthday, and although the 38-year-old Bob has always been irritated by his mother's overprotective attitude, he promises to visit, as he really is feeling quite ill and is beginning to consider his own mortality. As he waits for word from Owen, he sees that the apparent flu outbreak has made the news. Owen pays him a return visit, and as he checks Bob's throat, he catches a glimpse of movement, as if something is squirming beneath Bob's mucous membranes. Owen doesn't tell Bob, but advises him to remain quarantined at home. He also asks about Saskia Harden, implying that she may be the outbreak's patient zero, but Bob can't help Owen to find her -- and Owen's own throat is beginning to get sore.
Tosh detects more chronon discharges in the area of Garron Park, where a group of schoolchildren claim to have seen an old woman in the lake. Jack and Gwen head to the park to investigate, and see something burst up out of the water to decapitate a pit bull and disembowel its owner. They chase the creature away from the lake, but it turns and overpowers Jack, identifies itself as Sally Blackteeth, and tells Jack that his friend Professor Len is dead. The water hag then literally flies away, and Jack shoots after it as it goes; however, a policeman arrives on the scene, sees him standing over the bodies of a man and a dog while firing a gun, and shoots him. Owen arrives on the scene as Gwen identifies herself and Jack as Torchwood operatives, and to the astonishment of SOCO Sgt Kilshaw, Jack stands up, claiming that the policeman who shot him must have missed. Kilshaw has little choice but to cordon off the area and leave Torchwood to investigate, and as Tosh prepares a cover story, Owen informs Jack that he may have caught whatever's affecting Bob Strong.
Strong is coughing up bloody mucous when his doorbell rings. To his surprise, it's Saskia Harden, and she's holding her arm as if she's been shot. He tries to warn her that he's very ill, but Saskia simply tells him that she's here for her baby. Something squirms in the wound on her arm, and when Bob looks into her eyes, he sees that they're the colour of mucous. Meanwhile, Gwen, Jack, and Owen return to the Hub, to find that Tosh has started coughing up blood and has quarantined herself in the Hothouse while she tries to identify the pathogen. The few alien cells that she's found in her samples have mutated during her examination, as if trying to disguise themselves as human. Owen theorises that Saskia Harden infected everyone at Bob Strong's clinic, and that the Torchwood operatives caught the infection from the body Gwen and Tosh unearthed at Greendown Moss. Ianto is starting to cough up flecks of blood, and even Jack has a sore throat. Bob Strong then calls Owen, but is cut off while screaming Saskia's name, and Owen, Jack, and Gwen rush to Strong's house to find him lying half-dead on the floor. Before they can do anything, a homunculus bursts out of his throat, tearing his jaw and throat open and killing him on its way out. It flees through the open door before they can stop it, and Gwen and Owen see Saskia Harden standing on the other side of the road, holding it like a baby. Strong's phone then rings, and Jack is forced to break the bad news to Strong's mother.
It's now clear that everyone showing signs of infection is incubating a homunculus that will kill them when it's born. Jack, Gwen, and Owen return to the Hub, and on the way, they see that the police and EMT are out in force -- but many of them are also showing signs of infection. As they board the Hub's invisible lift, Gwen catches sight of Saskia Harden staring at her, and instinctively steps off the lift as it starts to descend; however, she loses sight of Saskia. Jack orders Ianto to help Gwen look for Saskia via the CCTV cameras around Roald Dahl Plass. Tosh confirms that the alien cells in her mucous are identical to the cells from the homunculus in the Greendown Moss corpse, but she then passes out. Fearing for her life, Owen scans her throat, but finds no sign of a homunculus -- and Tosh then revives and reveals that the homunculi only come to term in the presence of testosterone. Though weakened by the infection, Tosh is not carrying an alien parasite in her throat, and is able to return to work on a cocktail of drugs that should prevent the homunculi from growing to full term. Jack insists that she use him as a guinea pig, since he can always come back to life if she gets it wrong. Despite the risk, however, Owen orders Tosh to inject him with the drugs as well before his own parasite rips its way out of his throat.
Gwen is unable to find Saskia until the obvious occurs to her, at which point she becomes capable of perceiving Saskia standing on the invisible lift. Saskia confirms that she is the water hag known as Sally Blackteeth, and claims that she has come to colonise Earth because her own home planet, Strepto, disappeared while she was off-world. Gwen pulls out her gun, but another water hag -- possibly the one that Bob Strong coughed up -- comes up behind her and takes her by the throat, forcing her to drop her gun. More water hags approach her from all directions, and the other Torchwood operatives, seeing this on CCTV, realise that they've been migrating in towards the Rift for some time, spreading the infection as they approach. A policeman sees the group gathered around the water tower, and, assuming that they're women in fancy dress for a hen party, approaches to warn them about the curfew. As they tear out his throat, Gwen retrieves her gun and tries to flee, but the water hags regroup and recapture her. Saskia shrugs off her raincoat and her human form, and orders Gwen to take her into the Hub so she can access the power of the Rift.
Gwen tries to shoot her only to find that her gun has run out of bullets, and Saskia tears the gun out of Gwen's hand, ripping her flesh as she does so. Before she can do anything more, however, Jack, Owen, and Ianto arrive and inform Saskia that they've been cured -- and that Tosh is distributing the formula cure to the authorities. The men then open fire with MP5s, mowing down the water hags as they attack. Saskia leaps into Cardiff Bay, but Jack jumps in after her and wrestles with her as they sink deeper into the water. Tosh then calls the others back to the Hub, where the water hags are passing through the Rift and extruding themselves directly out of the water trickling down the tower. A giant, monstrous form then gurgles up out of the tidal pool, a huge body made out of mud and mucous, with Jack riding its back. Jack manages to pull back the monster's head, exposing her throat, and Owen opens fire with his MP5, decapitating the monster with the spray of bullets. Saskia had told Gwen that she was the only one of her kind, which means that all of the other water hags are her spawn; and since she came to Earth through the Rift, they're all linked to her via Rift energy. Saskia's remains disintegrate into the Hub's tidal pool, and the other water hags disintegrate along with her.
The situation resolved, Gwen calls Rhys to make sure that he's okay; he has come down with a sore throat, but has no idea what a close escape he's had. Gwen promises to return home to him once she's sorted out some loose ends at work, but as the Torchwood operatives recover from their ordeal, Tosh picks up a familiar energy spike in Leckwith. The lawyers from the Hokrala Corporation are sending another writ through to Earth, and Jack and his team must deal with it. It's just another ordinary day for Torchwood...