Merlin was a future incarnation of The Doctor hinted towards in Battlefield and elaborated upon in the target novelisation, The Tomorrow Windows and a bunch of short trips stuff. He is one of the many bullshit future incarnations of The Doctor that you can find if you keep digging through the Doctor Who EU rabbit hole.
He later got his own BBC show that was basically Smallville in Camelot. When that was canceled, he moved to America to become a supervillain played by John Barrowman. Does this mean that eventually, the Doctor will become the Face of Boe?