One of the biggest surprises in the Sherlock season 3 finale came at the very end of the episode, and showrunner Steven Moffat says it’s part of a larger plan.
Asked by Vulture whether or not Moriarty’s appearance at the end is a big plot point or just something to mess with people, Moffat replied, “I can’t really say what we’re doing with that, but there is no last-minute whim in this. We’ve had what we’re going to do with Moriarty in place from before the second season. Exactly what we’re going to do. I remember talking it through with Andrew Scott, who plays Moriarty. Wait and see what’s going to happen.”
These comments suggest that Moriarty may have deep ties to season 4, and that he is really back in physical form (or will somehow make digital appearances by a new villain in season 4 to mess with Sherlock).
Moffat also discussed the evolution of Molly from a one-off appearance to a regular. “She’s developed hugely,” he says. “She wasn’t even meant to come back after her first appearance, but she worked so well. Louise Brealey was so good. The girl with the unrequited crush became the first person to make Sherlock apologize in ‘A Scandal in Belgravia,’ and then you see it really shift around. Whereas all of Sherlock’s emotion on the rooftop when he’s talking to John in ‘The Reichenbach Fall’ is completely faked — he’s just trying to give his friend a bad time so he’ll be in an emotional state to believe what’s about to happen — the emotion when Sherlock turns up to Molly in that episode and says ‘I need you,’ I mean, it’s amazing everyone didn’t just get it right there.”
Read more with Moffat over on Vulture.