When Arthur challenged the Black Knight to a duel, Merlin went to the library to search for information on weapons that could kill the dead. He was assisted by Geoffrey, who showed him a fable about a sword that had been begotten in a dragon's breath. The story inspired Merlin to ask Gwen for the strongest sword her father had ever made. He then took the sword to Kilgharrah and asked him to burnish it.

Though reluctant at first, Kilgharrah agreed to burnish the sword after Merlin promised that it would be wielded by Arthur alone. Unfortunately, Uther and Gaius had already carried out their own plan to save Arthur's life by drugging him. Consequently, it was Uther, not Arthur, who wielded the sword against the Black Knight.

Kilgharrah was furious, claiming that in Uther's hands the sword would bring only evil. Because it could not be destroyed, he ordered Merlin to take it far away from Camelot, to a place where no mortal man would ever find it. Merlin later retrieved the sword from the armoury and cast it into the Lake of Avalon, where it remained for the next three years.

When Camelot was conquered by Morgause and Morgana's immortal army, Merlin, Arthur, and their allies were forced to go into hiding. Merlin took the Avalon Vial with him, which the Fisher King had said would provide help in Albion's hour of need. Merlin experimented with the vial using his magic, but whatever help it could provide remained a mystery until he accidentally broke it. Its water formed a small puddle in a crevice of rock and allowed him to contact Freya's spirit, who explained that the Cup of Life had made Morgana's army immortal by transforming them into the living dead. She also reminded Merlin that Excalibur was the only weapon that could kill the dead.

Freya retrieved Excalibur from the bottom of the Lake of Avalon and returned it to Merlin, who later willed the sword during Arthur's attempt to free his father from the castle dungeons. While searching for the Cup of Life with Lancelot, Merlin used the sword to kill many immortal soldiers and later used it to knock the Cup from its pedestal, spilling the blood it contained and destroying the immoral army.

When he had taken Merlin to retrieve the sword from the lake, Kilgharrah had repeated his warning that it could cause great evil in the wrong hands. He also made Merlin promise him that he would find a new hiding place for it when its task was complete. As such, after Camelot was retaken, Merlin took Excalibur to the Forest of Ascetir and placed it in a large stone.

One year later, Morgana launched a second attack on Camelot, forcing Merlin and Arthur to go into hiding. They journeyed to Ealdor with smugglers Tristan and Isolde, but were forced to flee from there as well after Agravaine and his men picked up their trail. Disheartened by yet another betrayal, Arthur lost faith in himself and felt that he didn't deserve to be king. To restore his confidence, Merlin located the rest of Camelot's survivors and gathered them together at the stone where he'd previously hidden Excalibur.

He took Arthur there the next day, and as they walked, he told him a story about how his ancestor, the first King of Camelot, had thrust his sword into a stone before he'd died. That way, if his lineage were ever questioned, the sword would form a test, as it could only be pulled free from a true King of Camelot. When they reunited with the others, Merlin coaxed Arthur into trying to pull the sword from the stone. He failed, but Merlin told him to have faith and to believe that he was destined to become Albion's greatest king. When he was sure that Arthur believed in himself, Merlin used his magic to help Arthur free Excalibur before all of Camelot's survivors.

Arthur later wielded Excalibur during his bid to retake Camelot from Morgana. He used it to kill dozens of Southron soldiers, including their leader Helios. Upon their return from Ismere, Arthur used Excalibur to appoint Mordred a Knight of Camelot.

Merlin (disguised as Dragoon) took Excalibur with him when he confronted the Dochraid about freeing Gwen from the Teine Diaga. When she refused to cooperate, he threatened her with the sword and slashed her arm, compelling her to tell him all that she knew. Later, when the Dochraid attacked him as he was leaving, Merlin responded by stabbing her, leaving her badly injured.

Excalibur was Arthur's weapon of choice in the Battle of Camlann. He fought many Saxons with it and later used it to kill Mordred, though not before being mortally wounded himself. Merlin later retrieved Excalibur from the battlefield along with Arthur and took it with them on their journey to the Lake of Avalon, where he hoped the Sidhe would heal Arthur.

They were ambushed by Morgana along the way, who attacked Merlin with her magic and taunted Arthur about his approaching death. Before she could do anything more, however, Merlin confronted her with Excalibur. Confident that no mortal blade could kill her, Morgana made no move to defend herself and was consequently killed when Merlin ran her through.

Merlin summoned Kilgharrah to carry them the rest of the way, but Arthur succumbed to his wounds before they reached Avalon. Heartbroken, Merlin cast Excalibur back into the lake and watched as Freya caught it in her hand and drew it back under the water. He then placed Arthur's body in a boat and set it adrift on the lake.