Deep in a subterranean cave, a beautiful witch molds a clay model into a tiny creature that she brings to life with a drop of water. She places the strange being into an egg and sends it hurtling down the river that flows towards Camelot. The egg surfaces in the water of a darkened vault - the one which supplies all of Camelot's drinking water.
There's a terrible sickness spreading through Camelot. Uther demands to know the cause. Gaius is forced to admit that it is a magical plague. Uther orders Arthur to find the culprit.
Merlin tells Gaius that if the plague is a magical illness, he wants to try to cure it with magic, but Gaius turns on him. If he's caught practicing magic, he will be killed. They need to use science to find the source of the disease so they can prevent it spreading. Meanwhile, Gwen discovers that her father has fallen ill with the disease. She goes to Gaius for help, but he can offer no hope of saving him. Merlin overhears this and can't help but be moved by Gwen's despair.
Merlin sets off into the street, evades a curfew and risks his life to go to Gwen's father. He disobeys Gaius's advice and secretly cures him with his magical powers. Merlin smiles and feels thrilled by his efforts then slips away into the night, unnoticed.
The next morning, Merlin's pleasure suddenly turns to shock as soldiers arrive and Gwen is arrested for using magic. She screams to Merlin for help, but a guilty Merlin doesn't know what to do. Uther quickly deems that she must be the sorceress who caused the sickness, then used magic to cure her own father of it. He sentences her to death. Merlin decides he has no choice but to own up. However, Arthur hears this and laughs at the idea. There's no way Merlin could be responsible - he's not a magician, he's a fool. He's only saying all this because he's clearly in love with Gwen! Merlin protests, but Arthur thinks he protests too much. A bewildered Merlin is released. Outside, he sees the flames being lit for Gwen's execution.
Gaius and Merlin are forced to use their powers of deduction to find the source of the disease. Together they trace the infection to the water supply in the vaults beneath the castle. When they go to investigate, the monster conjured by Nimueh lashes out, revealing itself.
Gaius identifies the beast as an Afanc, but he doesn't know how to kill it - and time is running out for Gwen. Merlin pays a visit to the Great Dragon and asks for his help. The Dragon replies that the key to killing the Afanc is to trust the elements at Merlin's command, but he will need Arthur's help. Merlin and Gaius work out that the monster is made of Earth and Water. The two other Base Elements - fire and wind - must be the key to killing it.
Help arrives just in time in the form of Morgana. Desperate to save her maid, she enlists Arthur to assist her. She, Arthur and Merlin go down into the Vaults to face the Afanc. The creature is terrifyingly fierce but the valiant trio triumph and the creature is vanquished.
With the monster dead and the sickness lifted, Uther grants Gwen her freedom, but Gaius has a secret to tell the monarch - he has discovered the egg which brought the Afanc to Camelot. It bears the mark of Nimueh, a great sorceress and Uther's mortal enemy...it is to be hoped Merlin's magic hasn't come to her attention.
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