A druid, Cerdan, and his boy apprentice visit Camelot to get supplies. When they go to the vendor, he gives them their order, and then apologizes. At first, Cerdan is confused, but then sees several Camelot guards rushing toward them and realizes the vendor turned them in. They flee, and during the chase a guard swings his sword and wounds the boy, whom Merlin telepathically hears scream in pain. Seeing that they're surrounded, Cerdan casts a spell to shut the barrier doors, which he tells the boy to run through. He escapes, turning to see the guard descending on his mentor.
Merlin telepathically hears the same voice calling for help. He steps outside and sees a boy huddled against a fountain, looking at him intently. Communicating telepathically, he tells Merlin the guards are after him to kill him. Merlin opens a door to the castle and tells the boy to run for it. He runs, but the guards spot him and give chase. Merlin bursts into Morgana's room, startling her and Gwen (Guinevere). Merlin explains what's happening just as a guard knocks on Morgana's door. Merlin hides with the boy while Morgana tells the guard she hasn't seen the druid they're looking for. The guards depart, and the boy faints, revealing he's wounded.
After King Uther orders Cerdan's execution, Prince Arthur privately asks if that's necessary since they were only in Camelot to get supplies. Uther deems it absolutely necessary because he used magic in Camelot, which is forbidden. Despite Arthur's protests that the druids are peaceful people, Uther fears they'd return magic to Camelot and believes they're conspiring against him under the guise of preaching peace. At Uther's refusal to appear weak, Arthur tries once more, saying that showing mercy can be seen as strength. However, Uther's convinced their enemies won't see it that way and wants to send the druids a message. He orders the city searched until the boy is found.
In Morgana's chambers, the boy has regained consciousness and lies in bed. In the courtyard, Cerdan's execution is taking place. King Uther announces Cerdan's crime of using sorcery in Camelot and warns that anyone harboring the boy will be seen as an accomplice and be executed. Standing at the executioner's block, Cerdan protests to Uther, "And let your fear of magic turn to hate. I pity you." Unable to watch, Morgana comforts the boy. Uther gives the order, and Cerdan is beheaded. Though he can't see what's going on, at the moment of execution, the boy screams telepathically and shatters a mirror.
Merlin asks Gaius about druids, but he doesn't know much as they're a very secretive people. Gaius becomes suspicious that Merlin's involved somehow. Being a terrible liar, Merlin admits to hearing the boy call to him telepathically. Gaius has heard of this, saying druids look for children with such abilities to serve as apprentices. He warns him to be careful while they're searching for the boy or his head could be next on the chopping block. Merlin assures him he will, but Gaius knows Merlin all too well and shoots him a warning look. Later, Merlin sees the guards searching every nook and cranny on their witch hunt.
Merlin returns to Morgana's room to check on the boy, who's sleeping. Worried, Morgana says he's pale due to loss of blood from his injury. She says he hasn't spoken yet, not even his name. Merlin points out the risk she's taking, being the King's ward. Morgana can't see the reason in executing an innocent child, suggesting that perhaps people don't choose magic, but it chooses them. When Morgana asks Merlin his reason for helping him, he says it was a spur-of-the-moment decision. Both agree that they need to return the boy to his people.
At dinner, Uther notices Morgana is troubled, but she assures him all is well. Arthur enters and reports that after a citywide search, they haven't found the boy. Convinced someone is hiding him, Uther orders him to double his efforts. When Arthur protests that he's just a boy, Morgana uncharacteristically sides with Uther, saying the druids are dangerous.
The following day, the boy has developed a fever. Morgana tells Merlin she fears his wound is infected and wants to fetch Gaius. However, Merlin doesn't want him involved, as it's too dangerous. Instead, he says he'll look for a remedy in Gaius' books to treat the boy himself. Arthur arrives to search Morgana's room, and in a magnificent bluff, she teases Arthur, even saying the boy's behind the screen, where he and Merlin really are. While they're distracted by bantering, Merlin uses magic to hide his boots, sitting in plain sight. Finally, convinced she's trying to make a fool of him, Arthur angrily leaves.
Gaius sees that Merlin's been reading one of his medical books and is delighted that he's taking an interest in his craft. He unintentionally delays Merlin by insisting he listen to his lecture about human anatomy. Finally, Merlin gets back to the boy and explains to Morgana why he took so long. The boy thanks Merlin telepathically, addressing him as "Emrys." When Merlin learns the druids call him Emrys, he asks the boy how they know of him. However, the boy doesn't answer.
Merlin visits the Great Dragon, who already knows he's here to talk about the boy since he too, can hear him. When Merlin asks about the name the boy called him, Emrys, the dragon tells Merlin he has many names, one of which is "Emrys." And, that much is written about him that he has yet to read. He tells Merlin he shouldn't protect the boy, which confuses Merlin, who says he's just like him. The dragon disagrees, comparing them to day and night. To Merlin's questions, "Heed my words," is the only response the dragon gives before flying away.
Gwen and Morgana care for the weakening boy, who speaks to Morgana telepathically. When Merlin arrives she begs him to get Gaius. With no other choice, Merlin tells Gaius, who's furious that Merlin put himself in such danger. However, at Merlin's pleading, he reluctantly agrees to help on the condition they get him out of Camelot as soon as he recovers. Since the guards are searching everyone leaving or entering Camelot, Merlin and Morgana decide to smuggle him through a secret door that leads to the lower town. The only problem is they must somehow get the key from Arthur. Merlin manages via magic to swipe it during Arthur's dinner.
A servant spots Morgana, cloaked by a hood, taking the boy to the door, and alerts the guards. Minutes later, Arthur sees the secret door's cover is exposed, and realizes his key is missing when he grabs for it. He sounds the alarms just as Morgana and the boy emerge from the tunnel. She stops by Gwen's house to pick up food, and the two elude the guards, led by Arthur, until they're cut off. Arthur orders the two to reveal themselves. He's shocked to see it's Morgana, who begs him not to hurt the child. After consideration, Arthur orders the guards to restrain them both.
Uther is beside himself when he learns that Morgana, whom he's treated like a daughter, has betrayed him. He accuses her of conspiring with the druids against him. When Uther orders the boy's execution, Morgana accuses him of being consumed by his hate for magic. He lashes out at her, grabbing her throat in rage at her insolence and says she will not speak to him until she apologizes for what she's done. Later, Morgana swears to Merlin that she won't allow the boy to die. Merlin agrees to help her.
Arthur tries to persuade Uther not to execute the boy, if anything for Morgana's sake. Uther is adamant that he should execute him now before he grows older and more powerful. When Arthur suggests Morgana will never forgive him, Uther angrily says he's not looking for her forgiveness, and only spared her because of the promise he made to her father to protect her. The boy on the other hand, enjoys no such privilege.
Morgana begs for Arthur's help to free the boy. At first, he's adamant that he can't change his father's mind, having already tried. Morgana, who knows Arthur disagrees with Uther, convinces him to do it for her sake. Merlin arrives, and Arthur tells him their plan. Merlin says it's too dangerous for Morgana. Arthur agrees, and comes up with a plan to free her of blame. He says she must apologize to Uther and be with him when the boy escapes. He volunteers a reluctant Merlin to help sneak him out through the burial vaults.
Conflicted, Merlin visits the dragon again to ask why he told him not to help the boy. The dragon says if the boy lives, Merlin can't fulfill his destiny. He hints that one day, the boy will kill Arthur unless Merlin allows him to die. Doing so will prevent a great evil. Merlin protests that the future isn't set, but the dragon doesn't waver, saying he must let the boy die. Later, Merlin cryptically asks Gaius if he'd let something bad happen to prevent something worse. Gaius says it seems Merlin's already made his decision. Merlin says, "I'm going to do nothing."
Gwen asks why Morgana is risking so much to help the druid boy. She answers that she feels an inexplicable bond with him, almost as if she was meant to help him. As planned, she dines with Uther and apologizes to him. Uther accepts, and wants to put the incident behind them. Meanwhile, Arthur releases a knockout gas into the guards' area so he can free the boy from the dungeon. He steals their keys and opens the cell, telling the boy not to be afraid, that he's sent word to his people and is taking him to them.
Arthur and the boy slip through the crypt tunnels as the guards recover from the gas, and realize their prisoner has escaped. They arrive at the gate, where Merlin is supposed to be waiting with a horse and hook to dislodge it, but he's nowhere to be found. Alone in his room, Merlin hears the warning bells, as does Uther. The guards move closer to catching Arthur and the boy as Merlin struggles with his decision to do nothing. Then, the boy calls to him telepathically, pleading for help.
Haunted by the boy's cries, Merlin meets them, saying he was delayed getting out of the castle. The boy eyes him suspiciously, as if he senses Merlin's lying. When riding off with Arthur, he bids "Emrys" goodbye, saying he knows that someday they'll meet again. Meanwhile, when Uther gets word that the boy's escaped with accomplices, he's livid. He warns Morgana that if she had anything to do with this, the punishment will be severe. When she denies it, Uther makes it clear that without a second thought, he'll break the promise he made to her father if he ever learns otherwise.
Arthur hands the boy back to the druids, who say they are forever indebted to him for returning the boy to them. Arthur asks them to never reveal that he helped them, and they promise to keep silent. As they leave, he calls out to them, asking the boy his name. The boy speaks aloud for the first time, "My name is Mordred." Arthur wishes him good luck.