Holmes returns to New York with a new apprentice and a renewed interest in working with the NYPD after being fired by London's MI6. Unfortunately, Joan, the NYPD's new go-to PI, must give her approval first.
When Holmes and Watson join forces on a double homicide, Sherlock's new apprentice, Kitty, threatens the investigation when she allows her jealousy of Sherlock and Joan's work rapport to override her better judgment.
Sherlock helps a math genius from his network of "Irregulars" experts after he stumbles upon a body while participating in a math puzzle competition. Meanwhile, Joan attempts to extend an olive branch after she learns about Kitty's past.
Sherlock and Kitty investigate after a man's severed hand is found in the street; Gregson gets in trouble with the brass and his daughter when he punches another cop; Sherlock discovers a manuscript that Watson has written about his cases.
A bored Sherlock forces his investigative services onto Joan, who is trying to locate a woman who has been missing for five years, and the only clue is the smell of nutmeg at the site of her disappearance. Meanwhile, Joan's bond with her long-distance boyfriend, Andrew, is tested when a man from her past reappears and asks for her help.
Holmes and Watson join forces with the NYPD after a police officer is murdered. Also, Sherlock searches for the creator of a "recovery blog" who is posting personal statements he has made in sobriety meetings.
When a nurse Watson used to work with asks for her help finding their missing acquaintance, the woman's trail leads Watson and Holmes to another person who has disappeared. Also, Sherlock struggles with his sobriety when he finds the recovery process monotonous.
While Kitty tries to find a runaway teen, Sherlock and Joan work a case in which the murder of a brilliant bioengineer looks to be at the hands of a drug cartel. Also, Joan makes a major life decision but worries it will impact Sherlock negatively, not knowing that Sherlock has big news of his own.
Holmes and Watson follow a blood trail into the world of wrongful death compensation when they investigate a series of murders in which the killer leaves envelopes of cash on the victims. Also, Holmes makes a generous gesture towards Watson as she suffers through the aftermath of a personal crisis.
A driver for a ride sharing company is intentionally run over by a city cab, Sherlock and Joan wonder if it's a case of professional jealousy. A romance Sherlock has with a longtime Irregular complicates when she makes a shocking request.
Holmes and Watson investigate the murder of a professional skeptic, a man who debunked paranormal, religious and scientific phenomenon for a living. The case becomes urgent when his homicide reveals a potential threat to homeland security. Also, Captain Gregson's daughter and fellow NYPD officer, Hannah (Liza J. Bennett), asks Watson for help with one of her cases.
Two New York City paramedics are shot and their ambulance with its patient is abducted by the murderer. Holmes and Watson join the manhunt to find out what happened and why. Holmes learns information about Alfredo, which strains their relationship.
When a judge is murdered, Holmes and Watson become involved in the interstate search to find the prime suspect, an escaped convict from a privatized prison. Also, when Holmes applies his deductive reasoning to Detective Bell's new relationship, the romance hits a rough patch.
A researcher - one of Sherlock's fellow beekeepers - who was investigating a deadly honeybee outbreak is killed; Capt. Gregson asks Watson for help with an unofficial investigation that helps him make a decision.