Tom, the father of Gwen, goes to work for a mysterious man who has been paying him to melt down lead. Before Tom's eyes the man produces a magical stone and uses a spell to turn the lead into gold. They are interrupted by Prince Arthur and the royal guards, who arrest Tom but fail to catch the sorcerer before he escapes. Meanwhile, Merlin has been awakened by the sensation that strong magic is at work.
King Uther charges Tom with treason for helping a known enemy of Camelot. The man Tom was working for is Tauren, who leads a notorious gang of wizards with the aim of bringing down Uther Pendragon. The king believes that Tom was supplying these sorcerers with weapons. Morgana fiercely denies these accusations but does not believe Uther when he says Tom will get a fair trial. Morgana tells him that if he kills Gwen's father, she will never forgive him. Uther then orders Arthur to hunt down anyone who has sheltered Tauren or his men.
Gwen tearfully visits her father in jail. He tells her he had no idea magic was involved and only wanted to give her a better life. Gwen is upset that he would turn to magic for money, but she swears to have him set free. She repeats everything he said to Merlin and Gaius, including the fact that a magical stone was involved and that Tauren had claimed to be conducting a scientific experiment. From this and the large gold piece that was found on Tom, Gaius rapidly deduces that Tauren was performing alchemy.
While visiting Tom's forge to look for Gwen, Morgana finds the stone that Tauren used. Gwen turns out to be resting at Gaius's house, and Morgana states to Merlin her belief that the trial is a formality and Uther plans to execute Tom anyway. That evening she goes down to see him in the dungeon, and gives him the key to his cell. Tom knocks out a guard and escapes but his disappearance is reported. Uther says the trial will now be a formality and gives the order for Tom to be killed on sight. Tom is eventually found by the guards, who execute him on the spot. Gwen screams in grief as his body is brought out.
Morgana furiously confronts Uther, who has her locked up. At Gaius's house Arthur tells Gwen that both she and her job are safe; she will not be thrown out of her home at the castle. He apologises for her father's death. Gwen returns to Tom's house but is viciously attacked by Tauren, who threatens to kill her unless she can find the stone and return it to him within the next two days.
Morgana is released from the dungeons at the request of Arthur, who promised Uther that she would not challenge his authority again. Gwen is upset to discover that Morgana spent the night in the dungeons on Tom's account. Morgana encourages her to go home and Gwen breaks down in tears as she explains that Tauren wants the stone. Morgana takes the stone and goes to the woods, where Tauren ordered Gwen to meet him, in Gwen's place. However, Merlin is awakened by the stone's presence and manages to follow her.
Tauren orders his men to kill Morgana but she hands over the stone and shows them that she has been chained up. She says she now wants Uther dead. Tauren explains that his plan was to use the stone to turn lead into gold, which he then wanted to use to bribe the royal guards to allow him access to Uther. Morgana decides that she would be far better placed to betray the king. Merlin visits the Great Dragon to ask for advice but is told to let Uther die, as it is Uther who persecutes the use of magic and whose reign must end before Merlin can achieve his destiny. Merlin still believes he cannot stand back and let Uther be killed.
Morgana goes to see Uther at dinner, initially pretending to apologise but she then becomes furious as she says he killed her own father. Uther had sent Morgana's father into battle and not sent him the necessary reinforcements as promised. Merlin asks Gaius if he thinks Uther is a good king, and Gaius states that, although at times his methods have been somewhat unsavoury, Uther has brought peace to Camelot and always tried to protect its people. He thinks that Arthur is too young and inexperienced for the responsibilities of a kingdom. Merlin refuses to explain the situation fully but Gaius says he trusts Merlin to make the right decision.
Uther summons Morgana and apologises for handling the situation with Tom insensitively. She suggests they visit her father's grave at first light and attempt to bury the past. Uther agrees and Morgana sneaks out to tell Tauren about this plan, unaware that Merlin has seen her. The next day, as they ride out, Gwen finds Merlin watching them from a window. She cannot understand why her father tried to escape the night before his trial but can only imagine it was because he knew he would be executed either way. Merlin asks whether she would kill Uther if she had the chance and Gwen, horror struck, replies that it would be murder. Merlin decides she is right. He takes his book of sorcery and the Sidhe staff that belonged to Sophia, and sets out after Uther.
At the grave of Morgana's father, Uther sorrowfully reminisces about his old friend. Morgana's father had saved Uther's life many times on the battlefield and was never afraid to question the king's judgement. Merlin confronts Tauren with the staff but is knocked out when Tauren uses the stone to reflect it back. He sneaks up on Uther just as Uther apologises to Morgana for having Tom executed, and promises to listen to her more. Tauren and Uther wrestle on the ground and Morgana stabs him which kills him. She and Uther embrace and decide to forgive each other.