Doctor Who secretly introduced the 45th - and final - Doctor, played by Colin Salmon. Doctor Who season 4 featured a chilling two-part story by future showrunner Steven Moffat. "Silence in the Library" and "The Forest of the Dead" are generally regarded as some of Moffat's best Doctor Who stories, and they certainly made their mark on the show, introducing viewers - and the Doctor himself - to Professor River Song. The Doctor and Donna found themselves dealing with the monstrous Vashta Nerada, creatures that had infested a planet-sized library created to provide entertainment for the VR consciousness of a little girl named Charlotte Lux.
Charlotte was supported by what appeared to be a mysterious but willful artificial intelligence named Doctor Moon, played by Colin Salmon, who seemed to be the mastermind behind the rescue attempt. Doctor Moon was a fascinating character, and in certain scenes he demonstrated a rather commanding presence. "There's the real world, and there's the world of nightmares," he told Charlotte at one point in a resonant scene. "What I want you to remember is this, and I know it's hard: the real world is a lie, and your nightmares are real. The Library is real. There are people trapped in there. People who need to be saved. The shadows are moving again. Those people are depending on you. Only you can save them. Only you." In the end, the VR environment became the home for River Song and a number of others who should otherwise have been killed by the Vashta Nerada.
Moffat and showrunner Russell T. Davies actually considered Doctor Moon to be the 45th - and final - incarnation of the Doctor. In Doctor Who Magazine #551, Moffat and Davies conducted an unusual mutual interview, and they discussed the twist. Moffat dug into his old files, and found an email that delighted him.
"In my head (and ONLY in my head, this will probably never appear on screen, or be confirmed in any way) River's not just [the Doctor's] wife - she's his widow. Somewhere in the terrible future, on a battlefield, the 45th Doctor dies in her arms and makes her the same promise she once made him - it's not over for you, you'll see me again. So River buries her husband and off she goes to have lots of adventures with his younger selves and confuse the hell out of them. Until, of course, she ends up in the data core of the Library Planet, and realizes she'll never see him again. And then she starts to wonder why anyone would call a moon 'Doctor'. Ahhh..."
Ironically, Moffat himself completely forgot this, and was only reminded of the idea by Davies. Showrunner back in 2008, Davies absolutely loved the idea. "I can't believe you didn't remember," he responded to Moffat. "I've never forgotten that Doctor Moon thing, it's so clever. Every time I watch that story, I think, it's him, it's the Doctor, and no one knows!" Colin Salmon plays the role perfectly, presenting a character who's deeply invested in saving lives, rather manipulative, and even tends to give lengthy monologues that should frankly intimidate a little girl. It's certainly easy to see him as a Doctor.
Moffat and Davies' revelation is highly unlikely ever to make it into canon - for one thing, fans can see traces of what would become the Battle of Trenzalore in Moffat's email - but it was certainly their intent when they crafted the story. As far as they were concerned, Doctor Moon was in fact the Doctor - the final, 45th incarnation of the renegade Time Lord who had saved the universe so many times in Doctor Who.