Season 2, Episode 1: The Curse of Cornelius Sigan
Original Air Date—19 September 2009

A treasure chamber is unearthed beneath Camelot,the centre-piece being the shining blue stone in the sarcophagus lid of Cornelius Sigan. Decades earlier Sigan was executed for sorcery and died vowing revenge.Greedy Cedric hears of the treasure and comes to Camelot. Learning that only Merlin and Arthur have keys to the vault he worms his way into the dim young prince's confidence and steals the keys, looting the chamber and stealing the stone. He is consequently possessed by Sigan's spirit, taking on his magic powers and animating gargoyles, which terrorize the city. In return for a promise that one day he will set him free, Merlin acquires extra powers from the Great Dragon and does battle with Cedric, saving Camelot once again. Given what has happened. however, Pendragon is more convinced than before that magic is only evil.

Season 2, Episode 2: The Once and Future Queen
Original Air Date—26 September 2009

Realising that 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 dual and lost, arrives at Camelot to kill the young prince. He enters the joust with a lance which has a dagger on its tip, but Merlin uses magic to defeat and kill Myror. Arthur has learnt some humility by his experience but tells Guinevere that Pendragon would oppose any romance between them.

Season 2, Episode 3: The Nightmare Begins
Original Air Date—3 October 2009

When Morgana sets her room on fire in her sleep she realizes she has magic powers and Merlin, against the advice of Gaius and the dragon, sends her to seek advice from the Druids. Pendragon, believing she has been abducted, orders the deaths of all suspected magicians unless she is returned so Merlin goes after her, locating her in the Druid village, where chieftain Aglain tells her the truth but gives her confidence that magic can be used for good. However, Merlin must get her back to Camelot before Arthur and a vengeful search party catch up with them.

Season 2, Episode 4: Lancelot and Guinevere
Original Air Date—10 October 2009

Gwen is mistaken for Morgana and kidnapped. Arthur heads out to fight for her freedom.

Season 2, Episode 5: Beauty and the Beast
Original Air Date—24 October 2009

Part One:-An ugly old troll drinks a potion transforming her 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 Pendragon 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 Pendragon and becoming the queen of Camelot.

Season 2, Episode 6: Beauty and the Beast II
Original Air Date—31 October 2009

Merlin spies on the troll and steals the potion she uses to make her resemble Catrina, replacing it with a fake one made by Gaius. Consequently she turns back into a troll, in view of everybody, but Pendragon, 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.

Season 2, Episode 7: The Witchfinder
Original Air Date—7 November 2009

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?

Season 2, Episode 8: The Sins of the Father
Original Air Date—14 November 2009

When a mysterious warrior challenges Arthur to a duel, no one could possibly predict the devastating chain of events that is set 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.

Season 2, Episode 9: The Lady of the Lake
Original Air Date—21 November 2009

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

Season 2, Episode 10: Sweet Dreams
Original Air Date—28 November 2009

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 with his jester, the wizard Trickler, but he is a disruptive force who wants to cause discord between Olaf and Pendragon to gain the 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 challenges Arthur to a dual. This time it is down to Guinevere, rather than Merlin, to break the spell.

Season 2, Episode 11: The Witch's Quickening
Original Air Date—5 December 2009

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. Merlin and Arthur pursue him, returning him and the crystal to court, though Mordred escapes and Morgana, having disowned Pendragon, 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.

Season 2, Episode 12: The Fires of Idirsholas
Original Air Date—12 December 2009

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 defenceless when the knights approach, intent on killing Pendragon. 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.

Season 2, Episode 13: The Last Dragonlord
Original Air Date—19 December 2009

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 and Pendragon persecuted these men years earlier and 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.