While hunting, Merlin and Prince Arthur are attacked by a giant scaled creature with the body of a leopard and the head of a snake. Merlin falls over while running from the beast and is nearly bitten, but they escape. Back at the castle Gaius informs them that the monster is most likely a Questing Beast, which, according to mythology, appears before a time of great upheaval. King Uther commands that it must be hunted down and killed at dawn. Gaius reminds Uther that it last appeared the night his wife died. At home he warns Merlin that a single bite from the creature is fatal.
That night Morgana has a horrifying nightmare involving Arthur and the creature. She runs out to Arthur as he is leaving, and begs him not to face the Questing Beast, but becomes hysterical and is dragged back inside the castle by guards. Merlin and Arthur trace the Questing Beast to a cave and are suddenly cornered by the creature. Arthur steps in to save Merlin, who was closer, and is bitten. Merlin uses magic to animate Arthur's sword without approaching the monster, and kills the Questing Beast. He drags the unconscious Arthur back to Gaius's house.
Gaius says Arthur will die and no magic can save him. A desperate Merlin visits the Great Dragon and swears he will do anything to save Arthur's life. The Great Dragon states that the Questing Beast was produced from the "Old Religion", which is "the magic of the earth itself". Merlin must go to a place called the "Isle of the Blessed", where he will find a way to save Arthur - and is warned that whatever the cost, Arthur cannot be allowed to die.
Merlin repeats to Gaius what he has been told about the Isle of the Blessed. Gaius cautions that because the Questing Beast chose Arthur, this means the Old Religion has decided Arthur must die, and if Merlin tries to change that, another life will be demanded in return. Merlin's mind is made up; he is willing to give his own life in exchange for Arthur's. The next morning he leaves for the Isle of the Blessed after asking Gaius to keep Arthur alive in the meantime. Arthur seems to sense that Merlin is in imminent danger, and becomes very agitated in his sleep, (like Merlin did in the Poisoned Chalice) again suggesting a magical link between them. Guinevere (Gwen) relieves Gaius from his watch at Arthur's bedside. She tells Arthur that she believes he will not die, and will one day be a very great and wise king who will bring peace to Camelot.
At the Isle of the Blessed, Merlin is confronted by Nimueh. He does not believe that the Great Dragon would have sent him to her but Nimueh explains she would not have tried to kill Merlin had she known his importance and asserts as she did before it is not Arthur's fate to die at her hand. She produces a magical cup blessed by the Old Religion; water from the cup must be brought to Arthur and he will be revived, but there must be a death in exchange. Merlin promises to give his own life for Arthur's, and fills the cup with rain from the sky. He brings the water back to Camelot and Gaius wants to know who will die so that Arthur may live, but Merlin does not answer.
Gaius gives Arthur the water from the cup. As he and Merlin leave, Merlin is intercepted by Morgana, who in a trance-like state warns "This is only the beginning." Later, Arthur awakes and Uther goes to inform the court that their prince will live. As Gwen changes linens in Arthur's room, he says he heard her talking to him when he was unconscious. She becomes very embarrassed and pretends not to remember what she said, though Arthur teases her and tries to get her to say it again. Merlin wakes the next morning to find his mother (Hunith) dying on Gaius's floor - Nimueh has taken her life rather than Merlin's. He visits the Great Dragon and angrily accuses the Dragon of sending him to "murder" his own mother. The Dragon tells him that his destiny is to protect Arthur until Arthur becomes king, at which point magic will be restored to Camelot and the Dragon will be free. Merlin resolves to ensure that the Dragon is never released; outraged, the Dragon tries to attack Merlin. Merlin tells the Dragon "you won't see me again".
Hunith is close to death and Merlin decides he must return to the Isle of the Blessed and restore her life by giving his. He visits Arthur and tries to say goodbye, promising to be Arthur's servant "until the day I die" also telling him that he believes that one day, Arthur will be a great king, Arthur is puzzled but touched by this declaration. At Hunith's bedside he says he will make her well again, in the absence of Gaius, who has gone out on an errand. Come morning, Gaius has not returned and Merlin finds a letter from him downstairs. In the letter Gaius writes that he has gone to the Isle of the Blessed in Merlin's place, as he is old and he does not believe his life held much purpose. He advises that Merlin will one day be the greatest wizard of all time if he follows Gaius's advice to be cautious with magic, and concludes Merlin has been like a son to him. Horrified, Merlin sets out after Gaius at once.
At the Isle of the Blessed, Nimueh expresses disbelief that Gaius would sacrifice himself for Merlin. She calls him a traitor who did nothing to stop Uther expelling sorcery from Camelot. Gaius explains his belief that Merlin is the only one who can return magic to the kingdom and will, with Arthur, make a better world. Merlin arrives just as Gaius has died. Nimueh says the Old Religion does not care who lives or dies, only that the natural balance of life and death is restored; however, Merlin retorts the choice is not that of the Old Religion, but rather that of Nimueh abusing her power. She wants Merlin to join her but he refuses to unite with such evil magic. They engage in a magical battle; Nimueh emerges victorious, having seemingly killed Merlin, and sadly muses that together they could have ruled the world. However, Merlin, who is still alive, rises and emphatically tells Nimueh: "You should not have killed my friend!" She is struck by lightning conjured by Merlin, and dies. Gaius awakens because her death has compensated for his own.
In Camelot, the Great Dragon rages against Merlin as Morgana wakes panic-stricken from another dream.