Arthur has been king for three years without incident, but now an expedition north to the land of Ismere, led by Gwaine and Percival, is captured by Morgana and fellow sorcerer Ruadan and set to work in the mines to locate a mystical key. A search party headed by Arthur and Merlin goes after them, coming upon a village whose inhabitants have been massacred, A dying Druid warns Merlin of Arthur's bane - a battle where the young king will be slain. Ruadan's daughter Sefa is a spy working as Guinevere's maid, who warns her father of Arthur's army heading for Ismere through the lands of his ally Queen Annis. The group is thereby ambushed and Merlin and Arthur captured by Mordred, whom Merlin recognizes from the prophecy as being Arthur's killer.

Ruadan rescues his daughter but is fatally wounded in the process. Merlin and Arthur are route-marched to Morgana's wintry hide-out. Mordred shows them some kindness but Merlin, having glimpsed the future, mistrusts him. Merlin and Arthur escape and arrive in the mines below the castle, where they free all the slaves and meet a spirit called the Euchdag, who is herself the Diamar, the "key" which Morgana had been seeking. Mordred saves Arthur from Morgana's attempt to kill him and is rewarded with a knighthood on the return to Camelot. Merlin remains wary despite the Euchdag telling him that Arthur's bane is Arthur himself, not Mordred.

Arthur rescues an old lady accused of sorcery, who gives him a horn with which to summon the spirit world. Despite Gaius's warning, he uses it to briefly meet his father but soon realises his error as Uther terms him weak for his non-political marriage, his practice of knighting ordinary young men on merit, and his lack of cruelty to make his subjects fear him. When Camelot falls prey to poltergeist attacks, with Guinevere the principal victim, it becomes clear that Arthur has unwittingly released his disapproving, vengeful father's spirit on the court. With a potion made by Gaius to make the spirit visible, and with Merlin's help, he sets out to return Uther to the grave, delivering a few home truths before it goes.

With the help of King Odin who blames Arthur for the death of his son Morgana invades the Kingdom of Nemeth in another attempt to take over Camelot. While Odin holds King Rodor of Nemeth hostage Morgana in disguise as a lady in waiting and Princess Mithian seek help from Arthur and his knights

The druid Osgar delivers the judgment of the disir to Arthur.

After visiting her father's grave, Guinevere is captured by Morgana and imprisoned in the infamous Dark Tower haunted by ghostly visions and screams. Merlin and Arthur lead the knights in a rescue mission but get lost in the thick and aptly named Impenetrable Forest. Mab, the fairy queen of this forest, appears to Merlin and shows him how to guide the others through it but tauntingly reveals that one will not return. Arriving at the tower, they save Guinevere but at the cost of a man. None, however, realise that Guinevere is a changed woman thanks to Morgana.

After Arthur is unseated from his horse, his saddle is shown to have been tampered with and stable groom Tyr Seward blamed. Imprisoned, he tells Merlin he saw the true culprit but was told his mother would die if he informed on them. The actual saboteur, Guinevere (enchanted by Morgana) kills Tyr, and Arthur realises too late his innocence. Guinevere then poisons Arthur and casts the blame on Merlin, leaving an imprisoned Merlin to use magic to save himself and the king. To cover herself, Guinevere summons the apothecary from whom Morgana purchased the poison to pass subsequent blame onto Morgana as the would-be assassin, though Merlin knows better.

Earnest young druid Daegal begs Merlin to come to his village and save his dying sister, but the boy leads him into a trap where he's left to die by Morgana. Arthur meanwhile hosts the ruthless Sarrum of Amata, with whom he plans to form an alliance; however, with Merlin deliberately put out of the way, the bewitched Guinevere, appealing to the Sarrum's lust for power, persuades him to assassinate Arthur on the promise of a share of the kingdom. He accepts (though plans on killing her, too). Guilt-ridden, Daegal returns to save Merlin and they make it back to Camelot in time to thwart the assassination, though with several casualties. Merlin is more determined than ever to discover the cause of Guinevere's unnatural actions.

Friendship, love, and loyalty between Arthur, Gwen, and Merlin.

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?