Nimueh, an evil sorceress and long-time enemy of King Uther, places a clay totem inside an egg and enchants it. The egg glows and the totem grows a heart that starts to beat. She drops it into a basin filled with water, sending it off on a journey. When it emerges in Camelot's underground water reserve, it begins to hatch. A man wipes his face with water from the pump. She grins, watching through the water in the basin, and says an incantation to bring a plague on Camelot.
Later, Gaius finds the man lying dead, face down in the village. He turns him over, seeing he's ghostly pale and his eyes are filmed over in white. They quickly cover him so as not to frighten the townspeople. Meanwhile, Gwen (Guinevere) visits her father, the local blacksmith, before work. On her way to the castle, she runs into Merlin and Gaius who are wheeling the covered body home. She tries to see what's under the cover, but Merlin distracts her with a little flirting to avoid raising suspicions. When Gwen gets to the castle, she gives Morgana flowers to cheer her up, as she hasn't been sleeping well lately.
Gaius examines the body and says he's never seen it anything like this illness. He concludes the man's disease was caused by sorcery -- and by someone very powerful. Before he can investigate further, Prince Arthur arrives and tells Merlin, who is blocking him from seeing the corpse inside, that Gaius has been summoned to appear before King Uther.
At the castle, Uther shows Gaius and Merlin a royal court member, dead from the same plague. Unnerved, Uther asks what the illness is. Gaius says it's killing people in 24 hours and spreading quickly. He points to sorcery as the likely cause. Uther orders Arthur to search every house in town to find the culprit before they're wiped out. He tells him to lend Merlin to Gaius so he can help him work on a cure. Uther cites this kind of magic as what undermines his authority and worries that if they don't find the sorcerer, people will turn to magic for a cure.
As Arthur and his guards search the town, Gaius and Merlin come across a plague-stricken man, still alive. Merlin wants use magic to help him, but Gaius forbids it as the guards are suspicious of everyone. It's not the time to be using magic. At home, Gaius is examining the contents of the man's stomach when Arthur and guards barge in to search the house. Arthur searches Gauis' books, then enters Merlin's room. Gaius discreetly asks Merlin about the whereabouts of his magic book. Merlin goes into his room and subtly uses magic to hide it out of sight while the young prince is distracted.
After they leave, Gaius wants Merlin to hide his book, but Merlin wants to use magic to help find the cure. Again, Gaius forbids it, as everyone in town is on a witch hunt. Merlin wonders how he's going to fulfill his destiny when at the time it's most needed, he's not allowed to use magic. Gaius tells him to be patient, his time will come. Right now, the only way to help is to use science to discover the source from where the plague is spreading. Meanwhile, Nimueh grins as she watches through her basin and sees her horrible creation swimming in Camelot's water supply.
Arthur's search yields nothing as the plague claims more victims, their draped bodies filling up Camelot's courtyard. Uther orders Arthur to impose a curfew and isolate the lower section of the city where most of the victims lived. When Arthur asks about the people who live there, Uther's at a loss to what else he can do. He must protect the city.
However, Gaius knows the plague is not spread through human contact because a royal courtier, whose body he's examining, wouldn't have been near the lower town. He helps Merlin deduce the cause, through science, that the disease is waterborne. On an errand to get a water sample from the lower town, Merlin sees Gwen running by crying, having just learned that Tom, her father, has the plague. Gwen begs Gaius to save him, only to have him tell her there's no cure. After she leaves, sobbing, Merlin wants to do something but Gaius, who starts to test the water, fears it's already too late.
That night, Merlin looks up a cure in his magic book and prepares a magical poultice. He uses magic to slip by the royal guards to Gwen's house in the lower city. He sneaks into their house, where Gwen has fallen asleep at her father's bedside. He places the poultice under Tom's pillow and says an incantation. The illness fades from her father and he wakes. Merlin watches as Gwen wakes and sees her father is better, smiling as they embrace each other at the "miracle."
The next day, as the body count grows, Gaius tells Uther that the source of the plague is the water pump that supplies the city. Uther tells Arthur to expand his search for the sorcerer into the surrounding villages. Merlin asks Gwen about her father, and then pretends to be surprised that he's recovered. When she says he doesn't seem surprised, she wonders how he knew. When Merlin jokes that he's psychic, she laughs.
Meanwhile, having heard about it, Arthur asks Tom about his recovery. Tom swears he had the plague, not some other illness, but doesn't know how he got better. In fact, he's fitter than he was before. When asked, he says Gwen was the only person with him when this happened. Arthur and guards search the house and find the magical poultice under Tom's pillow. Back at the castle, they arrest Gwen for witchcraft. Morgana protests her innocence, but Arthur's hands are tied. He can't turn a blind eye.
Merlin and Gaius see Gwen being dragged down a hallway, sobbing that she didn't do anything. Gaius ushers Merlin home and yells at him for the inconspicuous use of magic to cure one man. However, Merlin couldn't just let Gwen's father die. He rushes to court and watches hidden as Uther sentences Gwen to death. Morgana and Arthur protest her innocence, and say injustice is just as dangerous as magic. However, Uther only hardens, saying that Gwen played with fire, so she should die by it at the stake.
After getting a lecture from Gaius on the responsibilities of being a wizard, Merlin visits Gwen in the dungeon and promises he won't let her die. He barges into the king's council and proclaims he used magic to cure Tom. However, Arthur thwarts his gallantry, which he mistakes for lovestruck stupidity, by convincing Uther that Merlin is protecting Gwen out of love. At home, Gaius tells an angry Merlin that Arthur saved his life, and if they want to save Gwen, they must find out what's contaminating the water.
They go to the vault to get another water sample and discover the creature when it rises out of the water and roars at them. In his book, Gaius finds that the creature is an Afanc, an abomination that only the most powerful sorcerers can conjure. Seeking advice on how to destroy it, Merlin goes to see the Great Dragon, who cryptically tells him to use the elements available. He adds that Merlin is one side of the coin and Arthur is the other. Meanwhile Uther, desperate to stop people dying, moves Gwen's execution forward to that evening.
When Arthur tells Uther that his search has still revealed nothing, Uther, desperate to stop people dying, moves Gwen's execution forward to that evening. With help from Gaius, Merlin works out what elements the Great Dragon was talking about: Earth, Fire, Water and Wind. Since clay, from which the Afanc was created, is made from two of the four elements: earth and water, then he may be able to destroy it with the other two: air and fire.
When Morgana informs them that Gwen's execution was moved up, Merlin says he needs Arthur's help, but knows he won't disobey his father. Morgana says to leave that to her, and convinces Arthur to help through clever male ego goading.
Merlin, Arthur and Morgana go down to the vault where the Afanc lurks. When Arthur tells Morgana to stay back, she refuses, asking if he's afraid he'll be saved by a girl again. They hunt the slithery beast through the tunnels as it creeps in and out of shadows. When they split up, the Afanc attacks Arthur, who fends it off with his torch. Morgana and Merlin run to help, and Merlin screams at Arthur to hold up his torch. While everyone is distracted, he conjures a wind spell that turns Arthur's torch into a flamethrower that douses the Afanc with flames, destroying it. Nimueh, who is watching, curses Merlin for killing her creation.
Gaius goes to the king and shows him the pieces of the egg from which the Afanc hatched, pointing out Nimueh's mark on the shell. At her name, Uther shudders. Nimueh has wreaked havoc on Camelot before and Uther wonders if he'll ever be rid of her. He shouts at everyone to leave so he can ponder the gravity of the situation.
Her innocence proven, Gwen is released. Morgana credits Merlin for saving her even though he's too humble to admit it. Morgana tells Merlin that she knows his secret and that what he did is safe with her. Thinking she's talking about his magical wind spell, he becomes excited and wants to take her up on her offer to "talk about it." However, before he blurts it out, Morgana says Gwen is a very lucky woman, and her misunderstanding becomes clear.
At dinner, Gaius assures Merlin that one day people will recognize his talents, and, "They won't believe what an idiot you were," he chides. Meanwhile, as she angrily watches through the water in her basin, Nimueh swears revenge on Merlin.