Uther's daughter Morgana returns from banishment and poisons her father. Merlin arrives too late to save the king but gets Uther to acknowledge his illegitimate son on his deathbed. Merlin takes the boy to the ruined citadel of Camelot.

Morgana has trouble in her alliance with King Lot. Arthur acquires the sword in the stone and is crowned King.

Morgan invites Arthur to a feast and Merlin accompanies him. While the temptress delays Merlin, Arthur returns to Camelot drawn by his fascination with Guinevere. Meanwhile Kay and Leontes seek out a famed warrior to recruit him to Arthur's cause.

Whilst Guinevere wants to leave Camelot with Leontes he is obliged to stay as one of Arthur's knights being trained by Gawain, a brilliant strategist, who breaks Arthur's sword in combat. Having warned Arthur to resist his feelings for Guinevere Merlin sets out to have a new sword made by reclusive bladesmith Caliburn, a widower living with his daughter Excalibur. Caliburn's desire to give Arthur the sword he has fashioned himself leads to Merlin's destroying him with magic and, inadvertently drowning Excalibur, after whom he names the sword. Morgan, meanwhile, is struck down by a mysterious sickness and healed by Sybil, a nun who was once her teacher and knows all her secrets.

Arthur and his knights come to a village where the head man has been killed and his alleged murderer Colfur is about to be lynched. Arthur insists he is tried at Camelot as a precedent for a justice system to establish fairness. By getting Guinevere to talk to Colfur's little daughter he finds that the case is not as simple as it first appeared and he is grateful for her help. Sybil suggests Morgan adopt a charm offensive to win hearts and minds away from Arthur but it fails so she employs desperate measures to persuade locals they need Morgan's patronage. Merlin, still shocked by Excalibur's death, shuts himself away designing diagrams, which puzzle Uther's widow Ygrain.

Morgan impresses the supplicants who come to her court but is visited by a woman who claims Sibyl set fire to a convent in which her daughter died, requiring Morgan to punish the nun. Arthur accompanies Guinevere to visit her dying father, resisting further sexual temptations on the journey. Merlin leads Gawain, Kay and Leontes to recover books from Ector's house to start a library in Camelot. The young knights ask Merlin why he has eschewed magic and are told that the gift frightens him but he eventually uses it to help the injured Leontes.

Despite the misgivings of Ygrain and Kay, Arthur and his inner circle attend a banquet given by Morgan as a sign of reconciliation, during which her castle is attacked. Arthur's men prepare to defend it but Merlin is suspicious of Sybil as the 'attack' is evidently stage-managed by Morgan to break up the party. Merlin tells Ygrain Morgan killed Pendragon but asks her to keep the news from Arthur. Morgan overhears Arthur tell Guinevere he loves her, which she sees as her key to destroying him. After the 'enemy' has been repulsed Arthur and his party return to Camelot but Morgan has used magic to turn herself into Ygrain, keeping the genuine queen a prisoner in her castle.

Morgan fools everybody at Camelot with her disguise, even Merlin. However, after Redwald, a little orphan boy, whom she and Merlin have helped celebrate his birthday, accidentally dies because of her, Merlin has his suspicions. Vivian feeling sorry for Ygrain, releases her to confront Morgan but by this time Morgan, in her guise as the queen, has let slip to Leontes his wife's indiscretions with Arthur.

Morgan makes her escape, leaving a puzzled Ygrain believing she is going mad until Merlin explains Morgan's deception. They go to Castle Pendragon to confront her but end up as her prisoners. Leontes,now aware of his wife's infidelity,prepares to leave Camelot but joins Arthur and the knights in defending Bardon Pass,an outpost attacked by Morgan's men in Morgan's plan to show people the fragility of Arthur's protection and the need for her patronage. Guinevere also turns up and the affair is made public. The attackers are repulsed but Arthur stays behind to hold the fort,allowing the others to escape.

Morgan enters Camelot with her prisoners, claiming that they are traitors and that only she can save the realm from the marauding bands. Confronting Ygrain in private she kills her. Arthur does a sterling job of holding the attackers at bay using booby traps until his men return to rout the invaders though Leontes is slain. The knights return to Camelot where Sybil takes the blame for the conspiracy and is executed by an unconvinced Gawain. After Ygrain and Leontes have been laid to rest Arthur is free to rule with Guinevere, though Morgan, having sought advice at Sybil's grave, may not be willing to give in.