Joan meets with Kim Holder, a new client. Her sister, Jessica, disappeared five years ago. The only evidence was the scent of nutmeg. Five other women have disappeared under similar circumstances.

Sherlock is intrigued by the case and joins the investigation, against Joan's wishes.

They meet with the FBI agent heading the case, Blake Tanner. Sherlock believes Tanner is wrong. Pumpkin, the so-called serial kidnapper, doesn't exist. These disappearances were not committed by the same person and Sherlock is going to prove it. 

Sherlock discovers that Jessica had three keys that were the same make and model. Kitty and Watson find the third key opens the door to Noah Kramer, a shady defense lawyer she was having an affair with. He says he was working out of state when she disappeared. 

Sherlock discovers that Kramer told her that his client, Raymond Carpenter, was guilty of several murders and she was going to tell the police. Sherlock and Joan meet with Raymond Carpenter in Sing Sing. He admits Kramer told him about Jessica and he outsourced her murder. But the killer is dead.

They find a new crime scene with the scent of nutmeg. Sherlock brings in The Nose. He detects more scents, including sodium hydroxide. The murders are committed by different individuals but connected by The Cleaner. 

Sherlock, Joan and Kitty meet with Captain Gregson and Detective Bell to discuss their theory. Joan has some ideas on how to find them, but Sherlock says her ideas are dull. Kitty pretends to dead while Sherlock takes pictures of her to post on the Dark Internet.

Joan is reviewing records from Spaulding Technical Institute, looking for people who were certified in cleaning up crime scenes. Sherlock's plan got a response but when he meet with the "cleaner" it turned out he was an undercover cop.

Sherlock notes the ugly mural on the Spaulding Technical Institute flyer and figures out the artist is obsessed with nutmeg. Conrad Woodbine is their cleaner. 

Woodbine refuses to identify any of his clients. Sherlock notes that they will be difficult to find physical evidence but one of his client's might talk. They identify a possible client, a former head of the Armenian gang. They offer him immunity if he rolls on Woodbine.

They raid Woodbine's apartment but he's not there. Watson notes the scent of nutmeg. Sherlock starts digging in the sink's drain. Woodbine has been cleaned. 

Sherlock has Kitty dissemble the crime board. As she does, she finds a picture of Raymond Carpenter and the superintendent from Woodbine's apartment is in it. 

Joan and Sherlock meet with Carpenter again. His youngest son was Woodbine's apprentice and killed him on his father's orders. They tell Carpenter if he calls his son and tells him to work with the police, they will make sure he is safe. Otherwise, when other criminals find out about him, he'll never be safe again.