Sherlock faces the consequences of his relapse, and his father arrives to try to fix the situation. Joan and Sherlock, trying to get back on NYPD's good side, search for a missing woman working the theory she was killed by her husband.
When Morland offers to use his influence to have Sherlock and Joan reinstated as consultants to the NYPD, Sherlock's mistrust of his father makes him question his motivation to help. Also, with no work offers coming in, Watson wrangles a gig with the FBI investigating a triple homicide in a top secret research lab.
Sherlock and Watson are back working with the NYPD on a double homicide involving a doppelganger of the intended victim. Sherlock offers his consulting services to his father, to help him finish his business in New York.
When Holmes and Watson investigate the murder of a fertility lab technician, they discover the woman had a secret personal life that leads them to multiple suspects. Also, the tables are turned on Watson when she's investigated by an NYPD detective.
Sherlock and Joan investigate the murder of a struggling archaeologist who was seemingly killed for some vintage video games he unearthed. Sherlock sees Alfredo for the first time since his kidnapping.
A Russian billionaire is assassinated in New York and Holmes and Watson embark upon several instances of hacking and weaponory business. Meanwhile, a secret about Morland, Sherlock's father is revealed.
A social worker asks Holmes and Watson to investigate a private college, when she becomes convinced that they have murdered one of her colleagues. Sherlock uncovers more about the attempt on Morland's life.
When evidence at the morgue is destroyed, suspicion falls on emerging gangs. Holmes believes that identifying a Jane Doe will help him unlock the case, while Watson deals with the reappearance of an old adversary.
When Watson runs into Captain Gregson and his secret girlfriend, a former NYPD officer, she inadvertently sets the couple's breakup in motion. Also, Holmes and Watson investigate the murder of a wealthy woman who left her considerable estate solely to a beloved dog.
At the urging of Morland's wealthy associate, Henry Baskerville, Holmes and Watson look into the death of his brother and discover that a witness saw the man chased to his death by a large, glowing animal too fantastic to be real. Sherlock considers intervening when the trauma from the bombing at the morgue negatively impacts Dr. Eugene Hawes' work.
When Holmes and Watson are pulled into a double-homicide investigation, they discover the victims were staging a fake murder right at the moment they were killed. Also, Watson's inside man at Morland's office encounters a problem that threatens to expose her spying to Holmes and his father.
Sherlock's suspicions concerning Moriarty's handiwork turn out to be true and her evil successor is revealed. Morland's desire for vengeance causes Sherlock to consider just which brand of justice this new villain warrants.
Vikner's diabolical maneuvering to secure his position becomes known. Sherlock concocts a plan to unseat him only to unwittingly enable a power struggle, the ends of which he could barely have believed possible.