Merlin interferes and foils the attack, but Odin then corners the King in a gorge. In the second-season premiere, "The Curse of Cornelius Sigan", Cedric sought to gain access to Arthur's personal rooms in order to steal the keys to an underground burial chamber where a great treasure had been discovered. Morgana then sent Lancelot one final order via Agravaine - to kill himself, so that he would never reveal the plot to Arthur or anyone else. She managed to escape to Camelot, heavily traumatised by what she experienced, and managed to tell Arthur what had happened, as well as giving a vague description of the Dorocha. Arthur was deeply grieved by the loss of Lancelot, and even more so when Gwen later revealed that she had asked the knight to look after Arthur, indirectly inspiring him to sacrifice himself. It is Morgana's fury of constantly being thwarted by Emrys that fuels her to declare war on Camelot. When he is imprisoned and sentenced to death, it is later revealed that Gwen was the one responsible. She whispers that she thought she'd lost Arthur, her open affection surprising him slightly. Edwin then sent a magical beetle through Uther's ear to consume his brain. In "The Sword in the Stone, Part One", Arthur was ambushed within Camelot itself by an army led by Morgana and the warlord, Helios. Arthur did not remain regent of Camelot long after this when Uther was struck down by an assassin trying to kill Arthur in "The Wicked Day". Arthur, along with Merlin, Gwen, Tristan, and Isolde had to flee Ealdor when Agravaine caught up to them. Uther Pendragon (portrayed by Anthony Head) was the king of Camelot. It is unknown if he was good at sword fighting, but it is assumed that this would be the case since he appeared to lead from the front. Unfortunately, her curse resulted in the deaths of at least four people when she transformed during her two nights in Camelot, prompting an increased hunt for her. Fortunately, Merlin and Gawain were able to follow him and remove the bracelet, Merlin subsequently coming face-to-face with the Fisher King when he was trapped in the King's throne room after a door closed behind him. Gaius later finds out that Gwen has been put under the control of Morgana and vows to help Merlin uncover their betrayal to Arthur. Merlin becomes friends with Lady Morgana, the King's Ward, and Guinevere (Gwen), her maid. Merlin and Gaius quickly realized that the troll was an imposter when she refused a tonic Gaius had prepared for her, a tonic that, many years before, Gaius had used to ease the pain the real Catrina suffered from an incurable bone disease. She was arrested for witchcraft but later released, and joyfully reunited with her father. Shortly afterwards, when Merlin tried to use the reversing spell, it had no effect. Due to Arthur's essential role and the requirement that there be a sorcerer on hand to break the spell once Guinevere is in position, Gaius informs Arthur that he has found a woman to perform the task.

Her execution resulted in Mordred's defection to Morgana and the Saxons, bringing about their foretold alliance.

The man tells Merlin of Arthur's bane which he says "stalks him like a ghost", before showing him a vision.

Arthur is forced to execute Kara as an enemy of Camelot; it is this action which drives Mordred against Camelot and fuels him to join Morgana. Also, after he had been poisoned by Nimueh, he sent a light to guide Arthur out of the caves beyond the Forest of Balorand advised him not to take the Mortaeus flower despite the fact that without it he would die. Morgana's birthday arrives, and Arthur gifts her a dagger. As Agravaine and his men have found them at Ealdor, Tristan runs and hides in the woods along with Guinevere, Merlin, Arthur and Isolde. In "The Poisoned Chalice", Bayard and many of his knights visited Camelot with the intention of signing a peace treaty with Uther. Queen Annis (portrayed by Lindsay Duncan) is the widow of King Caerleon. He would not return to Camelot for some years.

Alator uses his magic to attack Morgana when she questions Alator on who Emrys is. In "A Remedy to Cure All Ills", it was revealed that his parents were killed during the Great Purge. They had already poisoned him and let Merlin take the fault for it.

Merlin talks to the Great Dragon and learns about his destiny to help Arthur become king and unite the land, allowing magic to come back. She ultimately fled, leaving Arthur once again in control of Camelot.

Agravaine smuggles Arthur's sword to Morgana who uses her magic to enchant the sword to bear the weight of a thousand ages. However, Merlin and Lancelot's deception was quickly discovered by Uther, who knew the man that Lancelot was claiming was his father, and the king ordered Lancelot's arrest. She tells Gaius when he notices her worry that they can never be, but Gaius comforts her by telling her to never underestimate the power of love. They found her after repulsing an attack by raiders and returned her to Camelot. However, she didn't know that she was dreaming of Dragoon The Great. In the battle Mordred succeeds in wounding Arthur, however Arthur then stabs him dead. He hunted Arthur in the tunnels, but was baited into chasing Merlin towards a dead end. He will go to extreme measures to protect those he cared about, even if it meant killing enemies. During the battle he was either unhorsed by Kilgarrah's tail or caught in the flames, but nevertheless, he survived.

With Gwaine having been injured in the fight, Arthur had him brought to Camelot to treat his wounds. He had a brief alliance with Morgana. Several weeks later, Morgause briefly slipped into Camelot itself when Morgana did not meet her for a pre-arranged meeting. In the episode "The Secret Sharer", seeking the true identity of Emrys, Morgana engaged his services in exchange for the healing bracelet Morgause had given her in the second season. The Witchfinder correctly suspects Merlin, Gaius and Morgana - his methods are unscrupulous, and in private conversation, it's intimated his techniques were more about power over people, specifically indicated in how he gets Gaius to 'confess'; he told Gaius that he knows Morgana also has magic of some sort, yet never voices this discovery to Uther. As Agravaine and his men have found them at Ealdor, Isolde runs and hides in the woods along with Guinevere, Merlin, Arthur and Tristan. After reuniting with a sizable force that included a large number of knights, including Leon and Percival, Arthur led them all, along with Merlin, Gwen, Tristan, and Isolde in an invasion of the castle.

After Mordred's appearance in "The Witch's Quickening," he disappears and he is not seen again until series 5, seven years later. Shortly thereafter, Morgause conspired with Cenred again, this time to bring about Arthur's demise. During the Great Purge, Uther contacted Balinor to express his desire to make peace with the Great Dragon. When they made a potion for Elena they had to use Gaius as bait to keep Grunhilda away from her so then they could give Elena the potion without Grunhilda seeing. Although Merlin had planned to leave Camelot with her, Freya attempted to escape on her own, not wanting Merlin to abandon his life for her, only to be cornered by Halig and Arthur's knights just before her transformation. Holding Uther responsible for the deaths of his siblings, Agravaine placed a charmed necklace on the dying Uther's neck in "The Wicked Day" that would ultimately be responsible for the king's death in that episode.