Bayard, the king of Mercia, comes to Camelot to form a union. However, before he passes the two ceremonial goblets for Uther and Arthur to drink, Nimueh, posing as a servant, takes Merlin to one side and tricks him into believing that the goblets' drink is poisoned. Merlin promptly disrupts the ceremony and is forced to drink from the goblet himself - if he lives, he will be turned over to Bayard to use as he wishes.
Merlin drinks from the goblet, and at first it seems like it isn't poison, but then he collapses. He is taken under the care of Gaius, who finds a poisonous flower petal in the chalice which has been put there by Nimueh. He explains to Arthur that an antidote can only be made from the leaves of this same mortaeus flower, a flower which may only be found in the caves beyond the Forest of Balor. Despite Uther forbidding it, Arthur takes it upon himself to find the flower.
In the forest where the cave is found, Arthur finds Nimueh disguised as a maiden, claiming to have been abused and abandoned by her master. Believing her story, he fights and defeats a cockatrice that guards the caverns. Afterwards, Nimueh tells him she knows where the flowers are found and leads him to them, only to cast another spell inside, causing the ledge he's standing on to collapse. Although Arthur survives by clinging to the cave wall and fighting off a giant spider, she leaves him there to die, telling Arthur that it wasn't his destiny to be killed by her.
While semi-conscious and under the effects of the poison, Merlin constantly mutters about Arthur's situation, suggesting he is either subconsciously using magic or has some kind of link with Arthur. Upon realising that it's too dark inside the cave, Merlin creates a sphere of ethereal light in his palm, which suddenly appears in a larger form near Arthur, hovering beside him to light his path. Arthur is soon attacked by many more spiders, but manages to reach across to pick the flowers needed to cure Merlin, and then clambers up the wall to the exit of the cave, guided by Merlin's light.
However, once Arthur returns to Camelot with the flowers, he is immediately arrested and taken to the dungeons. He begs Uther to take the flower to Gaius, but Uther, teaching Arthur a lesson in obedience, crumples the flower and drops it outside the cell. Arthur reaches through the bars to get it back.
Understanding that Arthur has returned, but also realising that no one is allowed to see him, Gwen poses as someone bringing Arthur's food in order to see if he had the flower. Arthur manages to secretly give her the flower, and Gwen returns to Gaius. In order to make the antidote work, Gaius secretly uses magic for the first time in the series, despite it being forbidden. Gaius then gives Merlin the antidote, and then his heart stops and when Gaius and Gwen embrace for believing that Merlin is dead, he suddenly awakes, and upon realizing Merlin is awake, Gwen kisses him in happiness. He does not remember anything since he drank from the goblet.
Upon discovering that the poison was made with magic, Gaius reveals to Uther that Nimueh must have been behind it, and the potential war between Camelot and Bayard's country is averted. Uther then reveals to Arthur that the woman he met was Nimueh, and emphasises how he believes all magic to be corrupt.