Okay! Another good one! Lots of Kitty character development! And Joan character development! And nutmeg. So, all in all, good stuff!
Joan is asked to investigate the disappearance of a girl that happened five years ago. Sherlock gets involved when he's interested by a strange detail in the case: at the scene of this woman's disappearance, people noted the smell of nutmeg. This same smell has connected several crimes over the years. Joan, Kitty, and Sherlock go to talk to the man in charge of the case, and Sherlock quickly deduces from the man's files that the "olfactory signature" is not from the murderer, but rather from someone who is called in to help clean up after crimes. Long story short, it was a man who used to work for the police to clean up crime scenes. He went rogue. They catch the culprit and all is well.
Meanwhile, we learn that Kitty used to play clarinet at an expert level. At the end of the episode, Sherlock praises her progress with her detective work, since she was the one who found a key clue to help them solve the case. As a reward, Sherlock tells her that she can play her music as loud as she wants instead of shutting it down. Kitty decides to put in some classical music, apparently reminiscing about her past.
Joan meets up with an old boyfriend who wants her help as a detective because his medical ID badge was stolen. Joan asks Kitty to take care of it, which she does, quickly. All of this makes Sherlock notice that maybe Joan isn't that happy in her current relationship with Andrew. It's true - Joan is getting frustrated because she and Andrew are basically in a long-term relationship for the time being. Sherlock notes that maybe Joan doesn't really want a normal relationship, and that she might be happier with some other arrangement wherein she only has casual sex or is free to pursue other partners. As Joan prepares a fancy dinner for her and Andrew, she laments that maybe Sherlock has a point.