We get a series of flashbacks showing Holmes meeting Irene Adler for the first time. She was a sexy American painting restorer in London, and her hobby was stealing classic paintings while giving her own work to the museums. They had dates where Holmes took her to the secret catacombs beneath London and compared her birthmarks to constellations. And then they had lots of sex… until Irene was replaced by a pool of blood on the floor.
In modern day, Irene is extremely freaked out, thanks to a year of sustained psychological pressure tactics performed by a mysterious Mr. Stapleton, who also left white peonies around the place for some reason. So Holmes attends to her every need while Watson handles the case solo. Irene had been painting with a very rare yellow pigment, which leads Watson to Isaac Proctor, a man who specialized in psychological pressure tactics for the CIA. Great! Except that the police get distracted talking to his brother and he escapes. And when he leaves a peony on Irene's bed, Holmes gets very concerned. He and Irene get ready to leave the country, but it's only until Watson completely eradicates Moriarty from the world.
But as soon as they are at the safe house, Holmes realizes that Irene has one of her birthmarks removed. And that's not something you do for a brainwashed hostage, so she must have been working with Moriarty! At this accusation, she leaves in a huff. So Holmes goes home, just in time for Isaac Proctor to shoot him. But then Irene appears and shoots Isaac!
Oh, and Irene is really British. And she's Moriarty. Shocking twist!
So that brings us to the second half of the two-hour episode, in which Holmes has to deal with a bullet wound in his shoulder. They stumble on some text messages sent by goons that Isaac killed in the first half, and that leads them to a Greek shipping magnate named "The Narwhal." All they can pin on him is a charge of smuggling lemurs, which isn't that big a deal. And in the time it takes to find out that Moriarty kidnapped his daughter, he gets out of jail. Holmes realizes that he's being forced to go kill some Macedonians in an elaborate scheme that will net Moriarty a billion dollars.
Holmes is unable to stop the murders, which sends him into a tailspin that results in an overdose. But when Moriarty stops by to gloat, it turns out it was all an act. So Moriarty is caught, and she has to deal with the shame that comes from having been correctly analyzed by Joan Watson, of all people. So she gets arrested and Holmes names a new species of bee after Watson. Good triumphs and evil is vanquished!
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The last episode ended with Watson and Holmes searching a big white house to discover Irene Adler, who's supposed to be dead. Holmes had a very short breakdown, but he's mostly recovered by the time this episode starts, one second later. Holmes runs to Irene and grabs her. She seems thrown by this. She claws at his face, but he embraces her anyway. Then she hugs him back. I guess I'd say that they have a complicated relationship.
And now we get to see how that relationship begins! The caption on the screen takes us to "London, a little over two years ago." We're in the season finale, so it's time to get some backstory on the season arc. You can't quibble with the construction of this story.
In London, Sherlock Holmes enters the home of one Irene Adler, who's played by Natalie Dormer with an American accent and a smirk. As soon as Holmes enters, he finds himself engaged in banter over the difference between a consulting detective and a private investigator. As she introduces herself, she praises the symmetry of Holmes's face. He's here to consult with her on a matter of forgeries of classic paintings. She says that the pictures he sent her aren't original Turner sketches. She knows this because they have a medium orange and an ochre, which, in 1839 required turmeric, which was confiscated by the British army at the time. So they're fakes. Holmes looks around at the paintings in Irene's flat and asks if she does original work. She says she's just a restorer because what could she add to such great work? He doesn't answer right away.
Holmes apologizes for lingering, then asks why there's an original Breughel on the wall when she was supposed to return it. He explains that she was supposed to restore a painting that was damaged by shelling, and she wouldn't have recreated the gouges on an imitation she painted for herself. So clearly she kept the original and sent a forgery to the museum. She says that the museum director wanted to file down the paint (I guess that's some kind of restorer sin), so she preserved the painting by keeping it safe. Holmes guesses that some of the other paintings in the room are also preserved. He offers to guess which ones are real, and if he's right, he gets a date with her out on the town. Plus, he's not going to turn her in because, "I appreciate your efforts to keep the vulgarities of the modern era at bay." He assures her they'd enjoy each other's company. She observes that he's not boring. Then she accepts his challenge -- but she wonders why, given the way he's looking at her, they'd need to leave the room to enjoy each other's company. Holmes likes the sound of that, so she takes his arm and he looks at the first painting.