When Holmes and Watson join forces on a double homicide, Holmes' new apprentice threatens the investigation when she allows her jealousy of Sherlock and Joan's work rapport to override her better judgement.
Holmes helps a math genius from his network of "Irregulars" experts after he stumbles upon a body while participating in a math puzzle competition. Watson attempts to extend an olive branch after she learns about Kitty's past.
When a ground breaking artificial intelligence software program is stolen, Holmes agrees to take on the case, but enlists Watson's assistance in solving it when he becomes more interested in disproving the computer's abilities than finding the thief. Meanwhile, Joan confronts Sherlock about his motives after she learns he has been in direct contact with her boyfriend, Andrew, without her knowledge.
Holmes and Kitty investigate the murder of a small postal store owner whose death is connected to the illegal diamond trade. Captain Gregson puts his career in jeopardy when he hits a fellow NYPD officer for harassing his daughter.
A bored Holmes forces his investigative services onto Watson, 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, Watson'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, Holmes searches for the creator of a "recovery blog" who is posting personal statements he made in sobriety meetings.
When a nurse Watson used to work with asks for her help finding a missing acquaintance, the woman's trail leads Watson and Holmes to another person who has disappeared. Also, Holmes struggles with his sobriety when he finds the recovery process monotonous.
While Kitty tries to find a runaway teen, Holmes and Watson work a case in which the murder of a brilliant bio-engineer looks to be at the hands of a drug cartel. Watson makes a major life decision but worries it will impact Holmes negatively, not knowing that Holmes has big news of his own.
Holmes and Watson delve 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. Holmes makes a generous gesture towards Watson as she suffers through the aftermath of Andrew's death.
Holmes is implicated in the murder of a woman who was killed during the height of his drug addiction. Holmes investigates to find the connection between himself and the victim, but the evidence begins to shake his confidence in his character.
After a driver for a ride sharing company is intentionally run over by a city cab, Holmes and Watson wonder if it's a case of professional jealousy. A romance Holmes has with a longtime Irregular is complicated when she makes an uncomfortable request.
When a member of Everyone is murdered, Holmes and Watson find themselves drawn into a civil war playing out on the Internet. Holmes is concerned that Watson's renewed dedication to their profession is turning her into him.
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. Captain Gregson's daughter and fellow NYPD officer, Hannah, 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 Llamosa, 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. Holmes buys a Stanley Cup and tests if it's the real one.
A researcher, one of Holmes' fellow beekeepers, who was investigating a deadly honeybee outbreak is killed. Captain Gregson asks Watson for help with an unofficial investigation that helps him make a decision.
Holmes and Watson take on an investigation of a personal nature when Holmes' friend and former recovery sponsor Alfredo Llamosa suddenly disappears.
Producers have tapped Raza Jaffrey as Joan’s new boyfriend, someone normal and stable and pretty much the opposite of Sherlock Holmes 
The series will jump ahead a full year when it returns in September, with Sherlock and Joan having been apart for nearly 12 months after the former left at the end of Elementary Season 2 for his new job at MI6.
Ophelia Lovibond joins the Elementary Season 3 cast as Kitty Winter, Sherlock's new apprentice. TVLine also reported Winter's relationship with Sherlock Holmes "will have ongoing repercussions for his relationship with Joan."
When the series returns on CBS later this year, Holmes will be "trying to get in Joan's good graces after almost a year away in London". TVLine reported, implying a possible year-long time jump in the Elementary Season 3 premiere.
it has been reported that the third season of Elementary will jump a whole year after Sherlock left to work for MI6 and Joan moved out from the house.