It has been a year since Lady Morgana disappeared and no trace of her has been found, as the fantasy drama starring Colin Morgan, Bradley James, Anthony Head and Richard Wilson returns for a new series. Just as it seems all hope is lost, Merlin and Arthur pick up a trail. Set upon by bandits it seems they may perish but Merlin's secret magic saves the day. As the dust settles, a mysterious, bruised and bloodied figure approaches the group: it's Lady Morgana. Camelot rejoices at her return but Merlin is worried that Morgana will remember the circumstances of their last meeting and tell King Uther that he tried to kill her. The King will not understand that he did it to save Camelot from Morgana's half-sister, sorceress Morgause's deadly enchantment; Merlin would be executed on the spot. Morgana promises Merlin that she has learnt the error of her ways and repents for the evil things she has done. Morgause no longer has any hold over her and Morgana forgives Merlin and promises to keep his secret. Uther and Morgana enjoy a tearful reunion. The King is delighted that his ward has returned and immediately announces a banquet in her honour. But is there more to her return than meets the eye? That night, Morgana slips out of the castle and journeys to a cave guarded by mysterious warriors. It seems that she has been playing a game. Far from renouncing magic she has spent the last year at Morgause's side. Morgana is no longer Camelot's daughter but a servant of the Old Religion. Using a handkerchief stained with Uther's grateful tears, Morgause concocts a spell to bring the tyrant King to his knees. As the evil magic begins to take hold of Uther's mind, Camelot is cast into great peril. Morgause is rousing Uther's mortal enemy, King Cenred, to invade the Kingdom, while Uther, plagued by hallucinations from his past, is incapable of mounting a defence of the realm. As Gaius urges Arthur to take command, Merlin begins to suspect that Morgana's repentance is not all it seems. He soon discovers he was right but the evil sisters are too quick for him. He is captured, bound with magic and left to the mercy of the scorpion-like enchanted serkets. As Cenred's army amasses on the border and Merlin's life hangs in the balance, the young sorcerer summons the Great Dragon, his last and only hope. Can the Dragon and the Dragonlord save Camelot from certain doom?

With Merlin gravely ill from the Serket's poison, Morgana and Morgause continue with their evil plan. They have mentally incapacitated Uther and convinced his enemy, Cenred, to invade Camelot. The fate of the kingdom now rests on Arthur's shoulders. The Prince and his Knights resist the invaders, but Cenred's soldiers are not the only threat they face. Can Merlin stop Morgana in time to save Arthur from the enemy within?