Young Merlin, sent by his mother from their village to start a better life, arrives in Camelot where he is to be apprenticed to Gaius, physician to the repressive King Uther. Uther, believing all magic evil, has made it punishable by death, so when Gaius finds that Merlin has magical, telekinetic powers, he agrees to keep the boy's secret. The mother of a sorcerer Uther recently executed comes to Camelot for revenge in the guise of a pretty girl, charming the court to sleep with her singing. Only Merlin sees what is happening and, staying awake, saves the situation without exposing himself as a warlock. As a reward, he is promoted to valet of Uther's arrogant son, Arthur.

Hearing that his village is being threatened by a warlord and his gang, Merlin travels home with Gwen, Morgana and Arthur, the latter doing his best to drill the peaceful villagers into a fighting force. Merlin's friend William is dismissive of Arthur's efforts, feeling they constitute egoism, though he ultimately saves the young prince's life. Nonetheless the villagers are inexperienced in martial ways and Merlin must use magic and conjure up a wind-storm to help see off the bandits.

The Questing Beast is on the loose near Camelot, and Arthur, ignoring a warning from Morgana who has dreamed that it will kill him, is bitten by the creature before Merlin slays it. Arthur sinks into a coma and the Great Dragon tells Merlin he can only save him by traveling to the Isle of the Blessed. On arrival there Merlin meets the witch Nimueh, who gives him the antidote, water from the Cup of Life, but warns him that, to save Arthur's life, another must be sacrificed. Arthur drinks the water and recovers but Merlin discovers the witch was not lying - his mother is consequently endangered. This will lead to the greatest ever test of both his emotions and his magic powers as he returns for a last show-down with Nimueh.

As Morgana's forces capture Camelot, Arthur at last comes to see his uncle's treachery. He is reluctant to flee, but Merlin bewitches him into escaping with him, temporarily blocking his memory and dressing him as a peasant. Elyan, Gaius, and Gwaine are taken prisoner, though Morgana is impressed by Gwaine's performance in trials by combat. Separated from Leon and Percival, Merlin and Arthur fall in with smugglers Tristan and Isolde, during which Merlin's spell wears off and the young king can reveal his identity to them. The quartet escapes to Ealdor, Merlin's village, where a wounded Arthur is nursed by Guinevere as Agravaine and his army close in.