The Duel between Merlin and Kilgharrah occurred after Merlin was advised by Kilgharrah to go to the Isle of the Blessed and seek out a High Priestess of the Old Religion in order to save Arthur's life after he had been bitten by the Questing Beast. That High Priestess, Nimueh, gave Merlin some water from the Cup of Life, which held the power to bring Arthur back from the brink of death in exchange for another life. Though Merlin had declared his own life as the sacrifice for saving, Nimueh had taken his mother's life instead, causing Hunith to suddenly become fatally ill. When Merlin discovered this betrayal, he became angry with Kilgharrah because the Dragon possessed the ability to foresee the things that have not yet come to pass, thus knowing when he advised Merlin to go to the Isle of the Blessed to save Arthur that Merlin's mother, or another innocent, would very possibly be sacrificed in Merlin's place.
Enraged, Merlin visited Kilgharrah and accused the Dragon of knowingly sending him off to sacrificing his mother's life. The Great Dragon responded by telling Merlin that it is Merlin 's destiny to protect Arthur until he becomes king, magic is restored to Camelot, and the Dragon is once again free. At this point, Merlin saw Kilgharrah's intentions and loyalties clearly, realising that Kilgharrah was ultimately self-serving and only concerned with being an ally to Camelot when doing so furthered his own agenda. Infuriated by this realisation, Merlin told Kilgharrah that, for his betrayal, Merlin would assure that the Dragon would never be released. Outraged, the Dragon attacked Merlin by breathing fire at him. However, Merlin blocked the flames with his magic. He then left the Dragon's Cave after saying: "You won't see me again" (Le Morte d'Arthur).
- Merlin, much to his resent, breaks his promise and seeks Kilgharrah's advice in the very next episode, the beginning of Series 2.
- The Great Dragon is also seen at the end of the episode screaming in rage. Just after that, Morgana awakes from a nightmare. It is unknown if she saw Kilgharrah in her dream or not. It may also be possible that she heard him.