While collecting wood, Merlin takes a moment out to produce a figure of a horse out of smoke. A woman rushes up Merlin and figures magic has been at work, whilst Merlin denies having seen anything in the smoke. Frightened, the woman ignores Merlin's pleas and runs to tell the King.
Arthur offers to find the source of the magic, yet Uther orders the services of the Witchfinder. Gaius attempts to sway Uther into using alternative actions, but Uther remains firm in his decision. In their quarters, Gaius advises Merlin to hide everything which could link him to magic. The Witchfinder, otherwise known as Aredian, arrives in Camelot and simply his presence frightens Morgana, who watches from her window. Uther explains to Arthur that Aredian works for nobody and is a law unto himself, before Aredian himself appears and states that Camelot stinks of sorcery. He also rejects the help of Arthur and his knights, favouring his own methods to root out the sorceror.
The next day, Aredian approaches Gaius in town and is introduced to Merlin. He requests Merlin's appearance in his chambers as he has some questions for him. During the questioning, Merlin denies having seen anything magical in the forest. Aredian remains unconvinced and asks Merlin to prove his innocence before letting him leave. In Uther's presence, witnesses brought to him give their accounts of other events of sorcery. Merlin is named as a suspect, much to Arthur's disbelief and Gaius' denial. While searching through Gaius' quarters, Arthur maintains the opinion that nothing magical resides there. Aredian is presented with a magical amulet and proceeds to leave to tell Uther, only to be told by Gaius that it belongs to him.
Returning to the chambers, Merlin is shaken to find everything in disarray. Uther is shocked at the concept that Gaius practices sorcery, however Aredian remains firm. In his cell, Gaius is interrogated by Aredian about his past. He is refused the basic needs until he confesses to practicing sorcery, yet Gaius refuses to do so. Merlin consults the Dragon, who tells him that if he confesses, Aredian would simply burn both Merlin and Gaius. He then tells Merlin that he cannot help him because he doesn't know how to, and that he is sorry; leaving Merlin almost in tears.
During his interrogation, Gaius admits to have treated Morgana. When asked, Morgana admits that Gaius had treated her for nightmares. Aredian permits Morgana to leave but asks if she knows what was in her potions, and that they could possibly be of magical content. Morgana admits that her nightmares had become worse since she was being treated; leading Aredian to awaken Gaius with the news that he, along with Morgana and Merlin, would die together.
Aredian throws Gaius in front of Uther, ordering him to confess, otherwise both Merlin and Morgana would die. Gaius proclaims he is the sorcerer responsible for everything Uther has been told and is sentenced to death the following morning. Angered, Merlin accuses Aredian of lying, only to be taken away by Arthur. Alone, Merlin tries fighting Arthur, but Arthur says that he isn't throwing him in jail, but breaking the law by letting Merlin see Gaius. Gaius states that he was trying to protect Merlin, and Merlin comes to the realisation that Aredian planted the amulet in their quarters as it didn't belong to him either. Merlin becomes enthused with the drive to prove Gaius' innocence, but Gaius warns Merlin he may die if he tries to do so.
As Morgana watches Gaius' stake being assembled, Aredian appears and takes her away for questioning. Gwen rushes to Merlin to inform him about this and Merlin reveals to Gwen that Gaius was set up. He rushes off to prove Aredian's guilt by sneaking into his chambers and rummaging through his things. Aredian returns to find his cupboard open and becomes suspicious, but doesn't find anyone in his room; although Merlin remains hiding underneath the bed.
In his quarters, Gwen and Merlin find an article which states that the petals from the flower Merlin found in Aredian's cupboard has the ability to produce hallucinations; meaning that the witnesses brought forward earlier were seeing visions and not actual events. Rushing into town, Gwen and Merlin go to a chemist who reveals that the Belladonna petals were given to him by Aredian, who threatened him with death if he didn't comply. Merlin sneaks into Aredian's chambers while he is sleeping and performs some magic. On the morning of his execution, Gaius awaits to be taken away. Gwen waits for Merlin to return while Aredian prepares for the day's event. Gaius is taken by the guards while Merlin prepares to go seek Arthur's help in delaying the execution. Gwen offers to go instead and they rush off.
In the city square, the people of Camelot gather to watch Gaius' execution. Arthur angrily demands that Aredian show Gaius some respect as Merlin and Gwen rush to the scene. As Gaius is placed at the stake, Gwen begs Arthur to stop the execution. Arthur is sorry but he states he cannot do anything as his father has already ordered the execution. Enraged, Gwen tells Arthur he can do the right thing and not re-enact past events by letting an innocent man die, referring to her own father's death. Gwen firmly tells Arthur to stop looking down at her as she knows she is a servant, but he should start wielding his powers as a Prince. Shocked, Arthur stops Aredian from torching the stake.
Before Uther, Merlin presents his evidence against Aredian. The witnesses admit to buying the Belladonna from the chemist, who in turn admits he got it from Aredian. Aredian denies the claims, yet Arthur defends Merlin and via a glance at Gwen, suggests a search be conducted in Aredian's chambers. The search reveals amulets inside Aredian's cupboards and as he struggles to deny his guilt, a toad emerges from Aredian's mouth, confirming to Uther and the guards he is a sorcerer. As Arthur, Uther and the guards advance on him, Aredian takes Morgana hostage at knifepoint but Merlin uses his magic to make Aredian's knife burn red-hot: staggering back in pain, Aredian stumbles over a chest, sending him falling through the window to his death.
With Aredian dead, Gaius proceeds with the cleanup of his chambers. Uther approaches him and offers the compensation of any breakages. He apologises to Gaius for suffering at Aredian's hands, but Gaius points out that he really suffered at the hands of Uther, and proceeds to berate Uther that his fear of magic has robbed him of reason, and that he is seeing enemies where none exist: he also remarks that while he has not been the first to be wrongly accused in Uther's war on magic, not all have been as lucky as him. A visibly shocked Uther assures Gaius that every measure will be taken to ensure the same kinds of events do not reoccur before leaving him to clean.
As they eat, Gaius and Merlin discuss the findings in Aredian's chambers. Merlin promises to never save Gaius' life again before he admits to putting the toad in Aredian's throat.