A treasure chamber is unearthed beneath Camelot, the centre-piece being a glowing blue stone in the sarcophagus lid of Cornelius Sigan. Decades earlier, Sigan was executed for sorcery and died vowing revenge. Greedy Cedric, hearing only of the treasure, comes to Camelot. Learning that Arthur has the one key to the vault, he worms his way into the dim young prince's confidence and steals it, looting the chamber and prying away the stone (which is actually Sigan's wicked soul). Consequently possessed by Sigan's spirit, Cedric takes on his magic powers and animates the castle gargoyles, which terrorize the city. In return for a promise to one day set him free, Merlin acquires extra powers from the Great Dragon and does battle with Cedric, saving Camelot once again. Given what has happened, Uther is more convinced than before that magic is only evil.

Realising that his jousting opponents always let him win because he is the royal prince, Arthur pretends to leave court and enters the lists in disguise to win on merit. He stays with Guinevere, who tells him some home truths about his arrogance, and they kiss. Moorish assassin Myror, paid by neighbouring king Odin (whose son challenged a reluctant Arthur to a duel and lost his life) arrives at Camelot to kill the young prince. He enters the joust with a lance hiding a dagger on its tip, but Merlin uses magic to defeat and kill him. Arthur has learned some humility by his experience but tells Guinevere that Uther would oppose any romance between them.

Morgana realizes she has magic powers when she sets her room on fire from her bed. Against the advice of Gaius and the dragon, Merlin sends her to seek advice from the Druids. Uther, believing she has been abducted, orders the deaths of all suspected sorcerers and their sympathizers unless she is returned, so Merlin goes after her. Locating her in the Druid village where chieftain Aglain tells her the truth (giving her confidence that magic can be used for good), Merlin must get her back to Camelot before Arthur and a vengeful search party catches up with them and kills all.

Gwen is mistaken for Morgana and kidnapped. Against Uther's wishes, Arthur heads out to fight for her freedom, with Merlin by his side to help him.

Part One: An ugly old troll drinks a potion transforming herself into the glamorous Lady Catrina, who arrives at Camelot with her servant Jonas. Gaius, who has met the real Catrina, and Merlin, who witnesses her true identity, are unable to convince bone-headed Uther of Catrina's real nature, especially when she bewitches him by giving him a magic pendant. Merlin attempts magic to expose her but she is too strong and it is too late to stop her marrying the king and becoming the queen of Camelot.

Merlin spies on the troll and steals the potion she uses to resemble Catrina, replacing it with a fake one made by Gaius. Consequently she turns back into a troll, in view of everybody, but Uther, still bewitched by her, fails to see this. Merlin learns that the only way to break the spell on him is to make him weep real tears. Thus Gaius prepares another potion, which Arthur drinks, and makes him appear to be dead. This does the trick and the king finally comes to his senses. Arthur kills the troll and Jonas and thanks Merlin for his efforts.

In his determination to rule magic out of Camelot forever, Uther hires the services of Aredian, a terrifying witch hunter who is most feared due to the fact that he stops at nothing in the quest to uncover all and every kind of sorcery. Even though no one is under direct suspicion, several people in Camelot are afraid that the witch hunter could see straight through them: Morgana is worried that Uther might have her executed and Gaius is concerned for the fate of Merlin and his own, since caring for the young warlock is considered crime and treason. Will all three be able to escape a dreadful fate?

When a mysterious warrior challenges Arthur to a duel, no one could possibly predict the devastating chain of events it sets in motion - least of all the young prince himself. Arthur and Merlin soon find themselves on a strange quest at the behest of the beautiful Morgause. Through her, Arthur discovers a dark secret which threatens to bring about the downfall of the kingdom.

Merlin saves a Druid girl from a bounty hunter's cage, but there is more to her than meets the eye.

Rulers from the Five Kingdoms converge on Camelot for a peace conference, including King Olaf and his spoilt, over-protected daughter Vivian. King Alined is also present, along with his jester, the wizard Trickler. He is a disruptive force who wants to cause discord between Olaf and Uther to gain ultimate power for himself. To this end he gets Trickler to bewitch Vivian and Arthur so that they fall in love and incur the annoyance of Olaf, who will challenge Arthur to a duel. This time it is down to Guinevere, rather than Merlin, to break the spell.

Mordred brings a warlock, Alvarr, to see Morgana, and they persuade her to steal a crystal with magical properties from the vaults of Camelot. Alvarr tells her it can be used to help people like themselves with special powers, though he really intends to destroy Camelot with it. Merlin and Arthur pursue him, returning him and the crystal to court. Mordred escapes, and Morgana (having disowned Uther), springs Alvarr from prison by drugging the guards. Merlin, having looked into the crystal, is alarmed by a vision of chaos, but Gaius assures him that it is far into the future.

Using an incantation, Morgause revives the deadly Knights of Medhir and, whilst Merlin and Arthur are the sole survivors of the party sent to beat the knights, Morgause uses Morgana to bewitch Camelot so that everybody except Morgana herself falls asleep, rendering the court defenseless when the knights approach, intent on killing the king. Merlin learns from the Great Dragon that the only way to break the spell is to kill Morgana, so he uses her as his bargaining power to force Morgause to call off the attack. As a consequence he must honour his pledge to free the dragon.

Morgana has gone with Morgause, and the dragon, freed by Merlin, repeatedly attacks Camelot, causing huge fire damage. Only a dragon-lord is capable of containing the beast, men whom Uther persecuted years earlier, from which only one still survives (Balinor), who lives like a hermit in a cave. Gaius, who helped him escape Camelot, tells Merlin this is his father, and when Merlin and Arthur trace him, Merlin reveals himself to Balinor (though they keep it from Arthur). Balinor agrees to come to Camelot to assist, but there is further drama before Merlin proves himself to be his father's son and defeats the dragon.