SPOILERS AHEAD
Well, that was an interesting episode!
The “bad guy” all season was revealed to be Charles Magnussen, an media tycoon who had a “mind palace”, in the same way that Sherlock does. Kept all his information there.
But was that really who was in charge of all this?
It was never directly shown, but I suspect that he had some connection with Moriarty. We saw at the very end that Moriarty is apparently still alive. If you recall at the end of season two, we saw Moriarty shoot himself, but the thing we did NOT see was blood. There was no blood pouring out of his head the way it should have been. Never saw his body taken away either, although that was implied.
It’s all sort of double reverse. Holmes was setting Moriarty up in Season 2, but Moriarty knew about it, went along with it and staged his death so he could turn the tables on Holmes later.
So.
Since Moriarty faked his own death, he would have stayed low, and found out pretty quickly that Sherlock was still alive. At this point Moriarty would need to “regroup”. He would let Sherlock dismantle all of his operations, since doing anything to prevent it would alert Holmes he was still alive.
While this was going on, he would stage a come back, planning revenge on Holmes. Perhaps even using Magnussen as an accomplice of sorts. Magnussen very nearly would have had both Watson and Holmes sent to jail, because he didn’t think Holmes would kill him. Probably wouldn’t have mattered to Moriarty either way, since either way, whether Magnussen lived or died, Holmes would be in jail.
Glad to see that Moriarty is back though. Definitely creepy character. Now all we have to do is wait for Series 4 of Sherlock! It can’t come soon enough.
Sherlock: Season Three