Moriarty (Scott) - the nemesis of Sherlock (Benedict Cumberbatch) - appeared to commit suicide in series two finale 'The Reichenbach Fall'.
Asked if the villain could have somehow survived, Scott told Digital Spy: "That's an impossible question to answer! It's very hard to come back from shooting yourself in the mouth, we all know that."
The Irish actor also admitted at the recent Arqiva British Academy Television Awards Nominations party that he had been overwhelmed by the "crazy" success of Sherlock.
"I think the quality of the show is even higher than last year," he said. "I've had... a lot more screen-time this year [and] 'The Reichenbach Fall' was a big Moriarty / Sherlock storyline, so it's been brilliant.
"The reaction to Moriarty has been incredible. I couldn't be more happy and more proud to be in the show. It's very difficult to find a popular and clever show."
"It might be a bit weird for the Doctor Who fans to have Moriarty coming up," he suggested. "It's a great show, but I think that might be a bit too weird for people to accept."
A third series of Sherlock will begin filming in January 2013.
The BAFTA Television Awards 2012 take place at the Royal Festival Hall at London's South Bank Centre on Sunday, May 27.
> Steven Moffat on Doctor Who, Sherlock and his BAFTA Special Award