This third intense season begins a year after the end of season two, with Arthur and Merlin searching for the kidnapped Morgana. Morgana has been raised by King Uther and is Arthur's adoptive sister, though it was revealed in season two that she's his half-sister. The two young men come across a camp of bandits and are attacked. After the battle, a worn looking Morgana steps out of the woods. They take her back to Camelot, where she recovers. Merlin is concerned she'll report him to King Uther because he tried to poison her when she became temporarily evil. Her magical powers were out of control and endangering the kingdom--and he thought that the only way to save them all. But Morgana really is evil and works with her sister, Morgause to take over Camelot. In fact, she personally kills two people with her own hand. She puts a spell on King Uther so that he begins to go mad. He begins seeing the ghosts of people he had killed during the Great Purge--when everyone who practiced magic was destroyed years before. Gwain, one of the future Knights of Camelot, is introduced and he's hitting on Gwen. Merlin again sees the future when he goes to a crystal cave and tries to prevent Morgana from stabbing King Uther to death. There are also episodes that involve Goblins, a Changeling and the search for the golden trident of the Fisher King. There is also an episode in which Gaius re-encounters the love of his life, a woman sorcerer who had fled during the Great Purge. She's being manipulated by a manticore into doing evil.
Morgana and her sister otherthrow King Uther and imprison him in his owndungeon, though his knights will not bow to her. Arthur, Merlin and old Gaius escape and try to figure out what to do. Merlin learns that if he empties the cup that gave Morgana's undead army "life" then they'll all die. And he gets the sword Excalibur from the Lady in the Lake and uses it to accomplish this task. The season ends with him putting the sword where no one can get it-- thrusting it halfway into a huge stone.
This is is definitely the best season of this show.