A rash of abductions of young boys that end up brutally murdered is plaguing London, and police are powerless to stop it. When William Moriarty discovers a clue linking all the victims, he and his brothers take an interest in the case.
In 1866, a brilliant young orphan and his ailing younger brother are taken in by a charitable aid organization, where they catch the attention of the son of an earl, who is discontent with Britain’s class system.
Albert invites the brothers to come live at the Moriarty’s estate, but the pair are not warmly welcomed by the other members of the household. Albert grows increasingly disturbed by his family’s intolerance, and resorts to drastic measures.
William begins teaching at a university, and is invited to dinner at the home of the Viscount of Belfor. He and his brothers receive a tour of the viscount’s well-kept conservatory, but are taken aback by what they hear of the gardener and his wife.
William learns that Lucian, one of his students at Durhnam University, hasn’t returned for three days. What’s more, the waitress Lucian had vowed to love throws herself from a bridge and dies. However, one of the university’s administrator assures William there’s nothing to worry about, but William disagrees and begins to investigate Lucian’s last movements.
A commoner is chased down by a hunter and his dogs before being shot. The ocean liner Noahtic begins its maiden voyage and Count Blitz Enders, an openly arrogant noble, heavily criticizes that commoners are allowed aboard. Days previously, William shared his plan to slowly remake society by plunging London into an era of crime, all while committing murders designed to educate commoners in exactly how the nobility have been abusing them, starting with Blitz.
Moriarty pretends to believe Blitz’s lie that he killed Thomas in self-defense and offers to cover up the crime.
Sherlock Holmes gets in trouble with his landlady Mrs. Hudson for not paying his rent. Holmes’ friend, Dr. Stamford, suggests Holmes get a flatmate and sends Dr. John Watson, whom Holmes deduces is a retired army doctor. Mrs. Hudson is impressed enough to allow Watson to become Holmes’ flatmate. Inspector Lestrade of Scotland Yard arrives and arrests Holmes for suspicion of murdering Count Drebber.
Sherlock and John, searching for the true criminal who killed Count Drebber, set a trap for the criminal using the wedding ring they found at the murder scene. Sherlock is able to deduce who the real killer is, who offers Sherlock a strange deal.
Sherlock is frustrated because he thinks there’s a mastermind behind the Noahtic and Drebber cases whose identity eludes him. Returning on a train after an unsatisfying investigation into another aristocrat’s death, he happens to meet William again.
With 48 minutes remaining before the train reaches the next station, Sherlock declares that William and he can find the murderer in time. Sherlock relies on the evidence at the scene, while William pursues a psychological profile of the killer.
Military Intelligence Service Director Mycroft orders Albert to recover classified papers that could rock the nation, and kill the woman who stole them. Sherlock is hired by the king of Bohemia to pursue Irene Adler, who threatens the king’s wedding plans.
Following William’s plan, Albert invites Irene to a masquerade, where a game with the famed “Lord of Crime” as its theme is being played. Dressed as a man, Irene uses the game to contact Albert, pleading for her safety in return for the stolen papers.
Despite Sherlock recognizing that Irene is dealing with the Lord of Crime, he sees her off. Irene negotiates with the Lord of Crime in an abandoned church, but before she can turn over the papers, Sherlock arrives, and makes a deal to keep Irene safe.
Receiving a new name, Bonde joins the Moriarty ranks, and is sent to retrieve the contents of a safe deposit box with Moran, Louis, and Fred. But when an unexpected bank heist spurs the others into spontaneous action, Bonde is left wondering what to do.
A series of murders is being carried out by someone claiming to be Jack the Ripper. In response, a vigilante group of the town's poor confronts Scotland Yard while William and the real Jack scramble to uncover the true culprit's aims and foil their plans.
A culprit is arrested in the Jack the Ripper case which was solved by the Moriartys. Suspecting a frame-up by Arterton, Lestrade asks Sherlock for help in finding evidence that would prove it. Meanwhile, Paterson works to sneak Bonde inside the station.
William outshined the adults in knowledge and nerve while saving the orphanage where he was staying. Judicial records state that William lent a nobleman £600 in the spirit of a certain play. But when the contract is broken, William takes drastic measures.
Adam Whiteley, a young MP in the House of Commons working toward an equitable society, garners public support as a "White Knight." Milverton is hired by those opposed to Whiteley to oust him. William takes interest in Whiteley, and decides to test him.
Whiteley goes alone to deal with the House of Lords with the irrefutable proof obtained from Albert in hand, but finds Milverton, the king of blackmailers. Even as Whiteley negotiates with him, Milverton's devilish clutches close in on his dear brother.
John introduces Sherlock to Mary, his fiancée. A stunned Sherlock realizes that Mary has another concern. She produces six pearls, detailing their connection to her missing father. She asks Sherlock to look into the matter, but is holding something back.
Milverton blackmails Mary, exploiting her dalliance in antigovernment activities as a student. Sherlock decides to sneak into Milverton's estate to steal his evidence, but even that act was anticipated. Sherlock finds that he is not the only trespasser.
When William James Moriarty claims responsibility for being the Lord of Crime in all the papers, aristocratic condemnation and public anger falls upon the Moriartys. The final problem of the Moriarty Plan that William has concocted at long last begins.
William aims to complete his plan with his death, as Albert and the others each carry out their roles. Meanwhile, Sherlock deduces William's true reason for having him vanquish the Lord of Crime. Overlooking London, the pair face each other one last time.