See, I feel that this is the sort of thing that can lead to a relapse. He was already under a great deal of stress, and the only thing keeping him sober was that he needed to be there for Irene... and now she's left him.
Holmes walks into the brownstone. He pulls Irene's sketches off the wall and calls Watson. Then he sees Isaac Proctor in the reflection of the lamp. Bang! Holmes has been shot in the shoulder. Isaac says they met once before, and then Holmes has pulled a stick free from the bannister and utilized his single-stick skills to free himself. He runs upstairs to the television room. He barricades the door, but this room doesn't have a window he can safely jump out of. Isaac says the other time they "met" was when he shot John Douglas (the contact for Gottlieb, Moriarty's accidental-death assassin) with a sniper rifle while Douglas talked to Holmes. Isaac gets into the television room and says that "she" tried to have him killed a few hours ago. Holmes is interested by the "she." And then! Isaac Proctor gets shot dead. Irene walks in. She says, in a British accent, "Bet you wish you'd run away with me when you had the chance." Holmes gasps, "Moriarty."
This is the halfway point in the episode, so it's a good place to take a break. I'd like to call your attention to the fact that the two different personalities that Natalie Dormer portrayed earlier were both phony characters put on by Moriarty. So if you didn't like her American accent (which I thought was pretty good, myself), that's on Moriarty. From here on out, she's playing an even more confident character than London Irene, although she'll be a bit less seductive. And I'll be calling her Moriarty from here on out.
Okay, on with the show. Moriarty tells Holmes that this isn't how she wanted to reveal herself to him. (Tee-hee). Holmes asks who the guy on the phone was that he talked to. She explains that it was a lieutenant who sometimes plays Moriarty. I think we all assumed that. Her customers sometimes need to feel that they're talking to a man, "As if men had a monopoly on murder." Holmes manages to sit up. She tells him that he doesn't want to believe her, "and yet your legendary powers of observation are screaming that I'm telling the truth right now." Holmes wonders what all the seduction and fake murders were about. He guesses that he interrupted her plans. Yes, there were several assassinations he messed up in London. Her first instinct was to quietly and discreetly murder him -- but then she became curious about his brain. She decided he was "something too complicated and too beautiful to destroy," so she studied him in his own environment.