An incarnation of the Doctor was one of many to have accounts claim that he would one day become Merlin. This version was seen when one of his previous incarnations looked into a Tomorrow Window.
Biography
The Doctor and his companion Anna travelled to Exeter in the 21st century where they encountered one of the Doctor's previous companions, Tegan, who cursed the Doctor for what her time with him had done to her. Later in the TARDIS, Anna found a diary that Tegan had kept during her travels in the TARDIS. The diary warned the reader that the Doctor manipulated his companions into killing for him. Anna realised that this had happened to her and asked the Doctor to take her home, which he reluctantly did. (PROSE: Good Companions)
After finding another companion, Guinevere Winchester, the Doctor was sent by the Time Lords to the Schrödinger Institute, a research station in deep space where sabotage had caused a temporal echo to occur. The temporal echo meant that the Doctor and Guinevere could not be seen by anyone or even touch anything until someone else did so. The Doctor managed to rewire a control box after a technician had worked on it. This broke the echo, allowing the Doctor and Guinevere to leave. (PROSE: Revenants)
Travelling alone, the Doctor went to visit his old friend, Greenaway. The Doctor told Greenaway that his life support machine was unable to keep him alive any longer. In an act of mercy the Doctor turned off the machine and left in his TARDIS, unaware that Greenaway managed to survive. (PROSE: Greenaway)
The Doctor once visited the Braxiatel Collection and found a diary in the archive that Jason Kane had kept whilst he was stranded in the past. The Doctor travelled back in time and brought Jason back to the future. The Doctor then kept Benny and Jason's wedding rings as a memento. (PROSE: The Collection)
According to some sources, the Doctor became known as Merlin, and resided in Arthur's World for some time. Merlin fought Morgaine in this reality on several occasions. After she bound him in ice in Breceliande, the Doctor summoned a dragon to melt it. Songs were sung among the people of the Doctor's "power over light, darkness and the elementals".
He taught King Arthur since he was a child, and saved his life on many occasions. When Arthur was old and had almost lost the battle to Morgaine, Merlin spoke with him of how the battle would end. Merlin took Excalibur from him and sent it back in time so that his previous incarnation would use it to defeat Morgaine. (PROSE: Battlefield)
Merlin later sent Excalibur to Winifred Bambera and Ancelyn so that they could prevent the Deindum from causing Phobos and Deimos to break away from their orbit of Mars. Because he needed to be "somewhere else", he used a hologram to speak to Bambera and Bernice Summerfield when they reached the chamber in which Excalibur could be used. (PROSE: Excalibur of Mars)
Appearance
This Doctor wore a mustard yellow waistcoat over a crumpled white dress shirt, open toed sandals and socks, bracelets, and a tatty Afghan coat. He had curly red hair and was very short. (PROSE: Battlefield, Revenants) He also had a strong scent of cologne. (PROSE: Greenaway)
Behind the scenes
Peter Anghelides has said this incarnation is partly based on one of his university friends and that he is meant to be the Merlin Doctor from Marc Platt's novelisation of Battlefield.[1]
However, the incarnation of the Doctor seen in the novelization is not the only one to have supposedly become Merlin. Muldwych long has been speculated by fans to be Merlin, and the Eighth Doctor took over the role in One Fateful Knight. The Tenth Doctor later claimed that he was once called Merlin by King Arthur. (COMIC: Fugitive)