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. However, Captain Gregson won't let him resume consulting for the department without permission from his former partner, Watson, the NYPD's new go-to private investigator.
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.
Holmes investigates when a groundbreaking artificial intelligence software program is stolen, but he enlists Joan's help after he becomes more interested in disproving the computer's abilities than in tracking down the thief. Meanwhile, Joan confronts Sherlock about his motives when she learns he has contacted her boyfriend without her knowledge.
Sherlock and Kitty investigate the murder of a small postal store owner whose death is connected to the illegal diamond trade. Also, Captain Gregson puts his career in jeopardy when he hits a fellow NYPD officer.
Holmes and Watson search for a thief who committed murder to steal a rare map. Meanwhile, Watson becomes concerned with Sherlock's escalating interference into Kitty's burgeoning personal life.
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.
In the first episode of a two-part event, Watson begins her new job as an in-house investigator for an insurance firm. However, her attention shifts to a case that is personal for both her and Holmes when they join forces to eliminate an imminent threat to Kitty.
As Kitty begins to unravel due to the imminent threat to her safety, Sherlock and Joan intensify their efforts to help her. Also, the origin of Sherlock and Kitty's relationship is revealed.
When a debt collector is murdered, Holmes and Watson attempt to narrow down a suspect pool of thousands of consumers who owed the man money. Meanwhile, Watson's relationship with Andrew progresses when he asks her to meet his father for the first time.
An unexpected event brings Watson into contact again with Elana March, the crime boss she brought to justice. Also, with Watson distracted, Holmes enlists Detective Bell to join him in a temporary partnership to solve a theft at a local zoo.
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.
When Holmes is implicated in the murder of a woman who was killed during the height of his addiction, he investigates himself to find their connection. As Holmes retraces his steps with Watson's help, the clues make his confidence in his own character waver.
Holmes and Watson investigate a murder that initially looks like a road rage incident, but takes a new direction when they learn the victim was flash-frozen at the time of death. Also, when Watson's mother finds out Joan's brother is cheating on his wife, she puts Joan in the awkward position of confronting him about the affair.
When a driver for a ridesharing company is intentionally run over by a city cab, Holmes and Watson wonder if it's a case of professional jealousy. Meanwhile, a casual romance Holmes has with one of his longtime "Irregular" consultants becomes complicated when the woman makes a shocking request.
Holmes and Watson find themselves in the middle of a civil war being fought on the Internet when a member of Everyone, the anonymous hacker group they periodically work with, is murdered.
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.
When two New York City paramedics are killed during a kidnapping, Holmes and Watson join the manhunt to find the murderer and the woman he abducted. Also, Holmes learns important information about his recovery sponsor, Alfredo, that 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.
Holmes and Watson look into the death of a member of Holmes' online beekeeping community who was a researcher looking into a deadly Northeast honey bee outbreak. During the investigation, they meet Tara Parker, a brilliant entomologist, academic and the leader of New York's beekeeping society. Also, Captain Gregson enlists Watson's services in an off-book investigation that helps him make a life-changing decision.
Holmes and Watson take on an investigation of a personal nature when Holmes' recovery sponsor, Alfredo, suddenly disappears. As they delve into Alfredo's life for clues, Holmes questions whether their friend has been abducted, or worse, if he suffered a relapse into addiction.