A druid, Cerdan, and his very young apprentice are in Camelot to collect supplies, but the shopkeeper reports them and they are chased by soldiers. Merlin telepathically hears the boy scream in pain as he is wounded by one of the royal guards. The druid is captured after using his magic to help the boy escape. Merlin now hears the boy's voice in his mind, begging for help. They manage to find each other by communicating telepathically, and Merlin hides him inside Morgana's room at the castle (having been told that the boy will be killed if the guards find him.) A soldier knocks on Morgana's door but she gets rid of him. She and Merlin then discover that the boy is wounded.
King Uther instantly orders the druid's execution. Prince Arthur protests that the druids are a peaceful people but Uther sees their use of sorcery as a threat. He wants to make an example to the druid people and orders the city to be searched until the druid's accomplice is found. The boy is recovering in Morgana's room and does not see what is going on, but at the moment of his master's execution he screams in horror and the mirror shatters magically.
Merlin later asks Gaius about druids and is forced to admit that he heard the child call to him telepathically. Gaius warns him not to be caught hiding the child, and says that druids look for children with magical gifts to serve as apprentices. Merlin later visits the boy, who is sleeping in Morgana's room. He refuses to tell her his name or even to speak. She is upset that Uther wants to execute an innocent child and says that magic may be something people are born with, rather than a choice they make. She and Merlin decide they must return the boy to the druid people.
At dinner Morgana is forced to make excuses when Uther asks if anything is troubling her. Arthur admits that the boy has not been found, and is ordered to continue the search. The following day the boy develops a fever because of an infection in his wound. Morgana wants to fetch Gaius but Merlin thinks this is too dangerous and offers to try and help the child himself. Arthur arrives with a guard to search the room. Morgana says that the missing boy is behind the screen (where he really is) and Arthur leaves, thinking she is making fun of him.
Gaius catches Merlin reading a book about medicine. He is delighted that Merlin is taking an interest, and insists Merlin sit and be lectured to about the human anatomy. Merlin finally gets away and goes to the boy. While Morgana fetches water, the child thanks him telepathically and calls him "Emrys." This is Merlin's name among the druid people. Merlin asks how they know about him but there is no reply. Later that night he goes to see the Great Dragon. The Dragon tells him that he has many names, of which "Emrys" is one, and is the subject of many prophecies that Merlin has not yet read. The Dragon, like Merlin, has heard the druid boy's voice. He says that Merlin must not help the child, but flies away without explaining why.
Meanwhile, the boy is being cared for by Gwen (Guinevere) and Morgana, and calls out to Morgana telepathically. He is becoming weaker. When Merlin arrives she begs for Gaius to be fetched. Merlin tells Gaius everything and Gaius is furious that he would put himself in such danger. Merlin says that the boy is dying and pleads with Gaius to save him. Gaius reluctantly agrees on the condition that they hand the child back to the druids as soon as he recovers. Everyone who leaves or enters Camelot is being searched, so Merlin and Morgana decide they will smuggle him out through a door which leads to the lower town. Merlin uses magic to get the key from Arthur.
Morgana and the boy escape but are seen leaving, and the guards chase after them. Arthur eventually catches them and orders them to reveal themselves. Morgana begs him not to hurt the child but Arthur tells the guards to restrain them both. The king accuses Morgana of conspiring with the druids against him. Uther commands for the boy to be executed and lashes out at her furiously when she says he has been overcome by his hate for magic. A tearful Morgana swears to Merlin that she will not allow the boy to die. Merlin agrees to help her.
Morgana asks for Arthur's help to free the boy. With Merlin they agree to carry him out through the burial vaults. Merlin again visits the Dragon and asks why he was told not to help the boy. The Dragon says that if the boy lives, Merlin cannot fulfil his destiny: the boy will one day kill Arthur unless allowed to die by Merlin himself. Merlin cryptically asks for Gaius's advice and Gaius says it seems that Merlin has already made his decision.
When Gwen asks why Morgana is risking so much to help the druid boy, she says she feels an inexplicable bond with him and believes she was meant to help him. As agreed with Arthur she goes to apologise to Uther in order to keep him distracted. Arthur uses a smoke bomb to distract the royal guards and then releases the boy from the dungeon. He has alerted the druids and they are waiting. The guards soon discover the boy is missing and raise the alarm. As the Dragon advised him, Merlin is not waiting to help Arthur and the boy escape. However, he is haunted by the boy's telepathic cries for help and runs to their aid. The child coldly promises "Emrys" that they will meet again.
Uther is furious to discover the boy has escaped. He threatens Morgana with death if he finds out she was involved. Morgana silently rages as he leaves the room.
Arthur hands the young boy back to the druids. As they leave he calls out to them, asking who the boy is. The boy speaks his first and only line aloud: "My name is Mordred." Arthur wishes him good luck as ominous music plays.