Morgana captures Alator - her former ally who later sided against her - in order to find out the identity of the legendary warlock known to the Druids as Emrys (still unaware this is Merlin). Merlin is approached by a mysterious woman, Finna, who warns him of danger and asks him to meet her at the temple of Erui. Though she is sent by Alator, Gaius suspects a trap and alerts Arthur to send his knights to find her, though she escapes with Merlin. She gives him a box and warns him against Mordred before willingly sacrificing herself to divert the pursuing Morgana. Back at Camelot, Merlin and Gaius open the box, which contains a prophecy of an imminent great battle. Shortly afterwards, a declaration of war by Morgana arrives.

Merlin sees Mordred helping Kara, a wounded Druid with whom he was once in love, but agrees to keep it secret. Later Kara tries to kill Arthur and is sentenced to death, with Arthur turning down Mordred's pleas for mercy. Mordred uses magic to help Kara escape but they are recaptured and Kara is executed. Merlin rightly fears this will make Mordred determined to destroy Arthur; and, sure enough, he flees and goes to see Morgana, revealing to her that Emrys is Merlin.

Merlin finds himself facing the future he's fought so long to avoid.

With Arthur's forces outnumbered, Merlin arrives in his guise as the aged sorcerer to defeat Morgana's army with magic. Arthur kills Mordred but is wounded and rescued by Merlin, who reveals that he is a wizard. Arthur is initially hostile but, advised by Gaius, allows Merlin to take him to the healing lake of Avalon. On the journey, Arthur comes to appreciate everything Merlin has ever done for him and eyes him with a new respect, even softening in his attitude to magic, but Morgana is pursuing them. Can they make it to Avalon ahead of her?