A bank teller calling herself Marie Samuels is dealing with an elderly customer, Mr. Venables, when two men with sawn-off shotguns enter the bank. Marie distracts the men by fiddling with her mobile phone, and sets off the alarm when one of the robbers takes her phone and smashes it. Furious, the robber tries to shoot her, but a young man in the queue wrestles the gun away from him. The police arrive, but arrest the young man, who’s still holding the gun. Marie and Venables try to explain what happened, but since young Josh is already under arrest, the police request that Marie come to the station to make a statement. Unfortunately for “Marie”, one of the policemen recognizes her as Sarah Jane Smith and greets her by name, thanking her for the help she gave the police while she was still working for Planet 3 -- back before some of the people she “exposed” turned out to be legitimate.

Sarah’s superior at the bank, Hedges, becomes worried when he learns her true identity, and as soon as he gets the chance he calls his associate, Harris. Harris, amused, advises Hedges to sit tight, assuring him that all will be different in the morning. Indeed it is, for after discussing matters with the CEO, Harris phones up Hedges again to inform him that his services are no longer required. Harris’ employers have already hacked into the bank’s servers, closed their accounts and withdrawn all of their support from the bank’s other financial ventures. If word gets out then Hedges will be ruined, but Harris simply hangs up, and when Hedges tries to call him back, he finds that none of Harris’ phone numbers are in service any longer.

Sarah returns to her flat, furious with the well-meaning policeman for blowing her cover; now she has to change her name and move once more, starting her life from scratch yet again. Her friend Natalie, a skilled computer hacker, promises to arrange for Sarah to get a new flat and credit cards within 24 hours. As Sarah begins to pack, Josh Townsend arrives to thank her for clearing things with the police; they were determined to pin something on him due to a shady past as a teenage arsonist, but thanks to Sarah and Venables’ statements, they’ve been forced to let him go... even though he couldn’t explain why he was in the bank although he wasn’t a customer. He admits now that he was looking for Sarah, to pass on a message from a common acquaintance -- Ellie Martin, who roams the countryside fighting the Establishment while Josh occasionally hands out leaflets for her in the city.

The next day, Josh accompanies Sarah to an Internet café to meet Natalie, a wheelchair-bound young woman with a talent for computer hacking. Natalie has already arranged for Sarah to get new credit cards under the name of Lila Quest -- and she’s also looked up Josh’s background and learned that, although his parents are rich, he’s turned his back on his privileges and struck out on his own. Sarah finds him trustworthy, and allows him to remain as Natalie informs her that her employment records have been erased from the bank’s servers -- and that a large amount of money was withdrawn overnight. Sarah contacts Hedges, bluffs him into admitting that he was involved in potentially fraudulent activities, and offers to give him the chance to tell his side of the story. Hedges agrees to meet her at the bank after hours, but contacts Harris and warns him. He’s afraid that Sarah will trick him into incriminating himself. Unfortunately for Hedges, Harris agrees, and promises to ensure that the interview never takes place.

Josh is impressed by Sarah’s skill at playing Hedges, but insists upon coming along, fearing that Hedges plans to set a trap for her. He’s curious about Ellie’s note, which asked Sarah to meet her at the village of Cloots Coombe, and mentioned something called “Operation Halter” which seemed to cause Sarah some concern. Sarah promises to explain this later, but first she visits the bank, only to find that Hedges has been shot through the heart and the head. Oddly, amongst his paperwork she finds a note about Cloots Coombe -- in somebody else’s handwriting, which suggests that her enemies are trying to lure her into a trap. Since this is her only lead, she decides to spring the trap anyway. Josh finally realizes that Sarah always suspected that Hedges was up to something, which is why she got the job at this bank in the first place.

Sarah picks up her trusty old VW Beetle, “Ethel,” from the garage where she’d hidden it, but while she’s packing up in her flat, someone apparently tries to steal the car -- which explodes moments later. Sarah and Josh thus head for the coach terminal, where Sarah finds that Hedges -- or his killers -- have closed out her current “Marie Samuels” bank accounts. Josh buys two tickets on the credit card provided by Natalie, and he and Sarah set off to investigate Cloots Coombe. On the way, Sarah explains that the final episode of her programme for Planet 3 exposed illegal activity at the Scottish fishery HalterCorp, but after broadcast, the evidence was proven to be fake. HalterCorp sued Planet 3 for making false allegations, Sarah’s contact at HalterCorp vanished, and not only did she lose her job with Planet 3, all of her official identity was invalidated by people in high places. Ever since then, she’s been trying to find out who set her up, and she started at Hedges’ bank, one of the branches of the company where she had her original accounts. So far, however, the link to Cloots Coombe is the only real lead she’s ever had...

At Cloots Coombe, the new Squire hosts a town meeting and assures the townsfolk that their long wait is finally over; tomorrow, a representative of the Company will be arriving from London to update them on the progress of the experiments. The Reverend Gosforth asks pointed questions of the Squire, but seems satisfied by the responses. In fact, he and the Squire are in league, and Gosforth is only making a public show of support to convince the villagers that he’s one of them. After the townspeople disperse, Gosforth finds the Squire examining the decomposing body of a young woman by the well. It isn’t the first body Gosforth has seen in this condition, but when he presses the Squire for an explanation, the Squire none-too-subtly threatens him should he continue to question what’s going on here.

Josh and Sarah meet Ellie Martin in the woods outside the village, and Ellie introduces them to Maureen Fletcher, or “Maude”, a cheerful elderly woman helps the well-meaning but disorganized protestors to plan their protests effectively. Ellie and Maude explain that a French company, Réchauffer Inc., has recently acquired a great deal of influence in the village -- and that badly decomposed bodies have been found in shallow graves, with evidence that they’ve only been dead for a very short while. Réchauffer has apparently been producing no industrial waste at all, a claim which the protestors find very suspicious. They’ve been trying to convince the villagers that the by-products from Réchauffer may poison the Well of St. Clothilde, a shrine which was once believed to have healing powers. However, not one of the villagers will support them, and Ellie suspects that they’re living in fear of the mysterious new Squire. All the protestors know for sure is that, despite the proximity of Salisbury Plain, the Ministry of Defence is not involved; they’re barred from conducting any experiments or weapons tests nearby due to a protest the villagers arranged 18 years ago.

One of the protestors, Jenny, has failed to return after trying to whip up support at the town meeting. Maude is unwilling to get the police involved, as they may take a dim view of the protestors’ activities, but Jenny still hasn’t returned the next morning. Sarah thus offers to inquire in the village, and lends Ellie her mobile phone. She and Josh enter the town, and Sarah soon spots something odd about the activity on the streets and the public noticeboard. She and Josh begin asking after Jenny, but the villagers are a tight-lipped bunch; Reverend Gosforth initially seems friendly, but he makes a hurried departure when they describe Jenny. He makes his way to the manor house to warn the Squire, but the Squire is already in a meeting -- with Mr. Harris, who is disturbed to learn that the Squire has been feeding more people to the monster in the well. They purchased Cloots Coombe to provide their company with a secure base for future projects, but it seems the Squire has become distracted by a sideline -- and the Squire is now arrogantly convinced that he personally, by controlling the creature in the well, will ensure their company’s success. Gosforth then arrives to warn the Squire that people are inquiring after the woman who died by the well last night. Harris recognizes his description of Sarah immediately, but the Squire is certain that he can take care of her...

Maude reluctantly decides to call off the protest in the light of Jenny’s disappearance, and Ellie tries to call Josh to let him know. However, he’s switched his mobile off again, as he doesn’t want it ringing at an inopportune moment. Natalie then calls, trying to get through to Sarah; she’s been conducting some research, and has learned that Réchauffer Inc. has set up shop in an old MoD base where the Ministry once conducted chemical weapons tests. The MoD were barred from Cloots Coombe after an accident occurred in the laboratories -- and Natalie has found out something disturbing about the average age of the villagers...

Sarah decides to visit the manor house and try to bluff the Squire into giving something away. Harris has gone by the time she arrives -- alone, claiming that Josh has given up and gone back to the protest camp. The Squire appears gracious and charming, but too much so, and Gosforth appears nervous as the Squire tells Sarah that Jenny left in a huff when none of the visitors would listen to her. Sarah inquires about the Well of St. Clothilde, the centrepiece of the village, and the Squire explains that though it was rechristened by the Church, its original name was “Old Clootie’s Well” -- after a nickname for the devil. It used to be a pagan shrine of healing, and there is still power there.

The Squire “offers” to let Sarah see for herself, and takes her and Gosforth to the well, where they hear something howling in the depths of the tunnel which connects the well to the old MoD base. Sarah has already worked out much of what Natalie is telling Ellie now, and the Squire confirms her suspicions; there are no children on the village streets and no notices of school events on the public noticeboard, because 18 years ago, a leak from the labs contaminated the well and all the villagers became sterile. Réchauffer has taken DNA samples from the villagers for use in cloning experiments, apparently to give the villagers a new generation of children -- but in fact this is merely a sideline. Their real intention is to breed an army of clones, infinitely replaceable soldiers with no families to mourn their loss. The initial experiments failed, producing a monstrous mutant which feeds on the life force, or the chi -- but the Squire sees this as a success, and he believes that the monster is under his control, and that his “perfect soldier” will kill anyone who gets in his way. He prepares to feed Sarah to the creature, but at the last moment Josh arrives; rather than returning to the camp, he’s in fact brought his old arsonist’s skills into play and set fire to the Réchauffer laboratories. The building explodes, and the fire sweeps along the tunnel up out of the well, immolating the mutant and killing the Squire as he rushes forward to protect his “child”.