Merlin's Death
In the version of the tale written by Geoffrey of Monmouth and Mace, Merlin had already disappeared by the time Arthur was born. Merlin did not even play a very significant role in his conception. Most versions write that Merlin outlived Arthur and told Percival that he would live until the end of the world. In other versions, the death of Merlin is caused by the Lady of the Lake, whose name (though there are various versions) is Niniane. Sometimes she was written as a maiden, sometimes a fay, but either way, she trapped Merlin in a rock with her enchantment after learning some of his magic and deciding to use it against him. (1)

Some major differences arrived with Geoffrey of Monmouth's and Wace's tales of the legend. Romances were expanded and elaborated on. Completely new adventures were added to the story, which included the addition of new characters who had never been seen before in the legend. Surprisingly, Arthur and Gawain had been so drastically altered that other heroes such as Lancelot, Galahad, and Tristan had a larger role than even Arthur himself. (2)

Links
(1) www.timelessmyths.com/arthurian/merlin.html
(2) http://www.timelessmyths.com/arthurian/vulgate.html