Young Sherlock Holmes
Teenagers Sherlock Holmes and John Watson meet and become good friends as students at Brompton Academy, a school in London. Watson is introduced to Elizabeth Hardy, who is Holmes' love interest. He is also introduced to Rupert T. Waxflatter, Elizabeth's uncle, a retired Brompton professor and inventor. Holmes is close to Professor Rathe, his fencing instructor, who warns Holmes that he is too emotional and impulsive.
Meanwhile, a mysterious hooded figure uses a blowpipe to shoot Bentley Bobster and Reverend Duncan Nesbitt with hallucinogenic thorns, causing the men to experience nightmare-like hallucinations resulting in their deaths. Holmes suspects foul play about the murders, which were presumed as suicides, but is rebuffed by Scotland Yard policeman Lestrade when he suggests a connection between the deaths. Holmes is later expelled from Brompton after getting framed for cheating by his rival Dudley. As Holmes reluctantly prepares to leave, Waxflatter is shot with a hallucinogenic thorn and accidentally stabs himself while trying to fend off imaginary gremlins. As Waxflatter dies he whispers the word "Eh-Tar" to Holmes.
Holmes secretly meets with Watson and Elizabeth and begins his investigation with the murders. During their investigation, the trio uncover the existence of Rame Tep, an ancient Egyptian cult of Osiris worshippers. The cult's main weapons were blowpipes, which were used to shoot thorns dipped into a solution made of plant and root extracts which, when injected into the bloodstream, causes the victim to experience realistic, nightmare-like hallucinations. Holmes, Watson, and Elizabeth then track the cult to a London warehouse, where the Rame Tep are performing human sacrifices in a secret underground wooden pyramid. After they interrupt their sacrifice of a young woman, the Rame Tep chases the trio and shoots them with thorns, but the three manage to escape into a cemetery. They begin to experience hallucinations (Elizabeth is being chased by the undead, Watson is force fed by sentient pastries, and Holmes' dead father is angry with him for uncovering his adulterous life), but Holmes is able to keep them all level-headed and they survive.
The following evening, at Waxflatter's loft, Holmes and Watson discover a picture of the three victims and a fourth man, Chester Cragwitch, who is the remaining victim. However, they are discovered by Professor Rathe and Mrs. Dribb, the school nurse, who plan to expel Watson and Elizabeth in the morning. That night, while Elizabeth heads to Waxflatter's loft to salvage his work, Holmes and Watson head to see Mr. Cragwitch, who explains that in his youth he and the other men had discovered an underground pyramid of Rame Tep and the ancient tools of five Egyptian princesses while building a hotel in Egypt. Their find led to an angry uprising by the people of a nearby village which was violently put down by the British Army. The men returned safely to England. However, a local boy of Anglo-Egyptian descent named Eh-Tar and his sister vowed revenge against them after their parents were killed in the attack. They also vowed to replace the bodies of the five Egyptian princesses. Cragwitch is then shot by a poisoned thorn and tries to kill Holmes, but is knocked unconscious by Lestrade who reconsidered Holmes advice after he himself was accidentally poisoned by the thorn.
As they return to the school, a chance remark by Watson causes Holmes to realize that Eh-Tar is none other than Professor Rathe, but he and Watson arrive too late to stop him and Mrs. Dribb, who is revealed to be Eh-Tar's sister, from abducting Elizabeth. Using Waxflatter's latest invention, a flying machine, Holmes and Watson travel to the warehouse just in time to prevent Eh-Tar from sacrificing Elizabeth as the fifth and final "princess". They burn down the Rame Tep pyramid and Mrs. Dribb accidentally swallows one of her poisoned thorns in a fight with Holmes and is burned to death, but Eh-Tar escapes with Elizabeth. Watson successfully stops Eh-Tar by sabotaging his carriage. Eh-Tar then tries to shoot Holmes, but Elizabeth intervenes and is mortally wounded instead. Enraged, Holmes duels Eh-Tar and manages to get the better of him when Eh-Tar falls through the frozen River Thames. Holmes returns to Elizabeth's side and holds her as she dies.
Afterwards, Holmes decides to transfer to another school to get his mind off Elizabeth. As he exchanges goodbyes with Watson, Holmes explained how he deduced the identity of Eh-Tar. Watson also points out that "Rathe" is "Eh-Tar" spelled backwards, a clue that Holmes failed to notice. Watson gives Holmes a pipe as a Christmas and farewell present. As Holmes leaves with his new detective outfit, Watson's older self (the Narrator) expresses that he was certain he would have more adventures at Holmes side.
In the post-credits scene, Eh-Tar is revealed to be alive; he checks himself into an Alpine inn with a new name, "Moriarty", foreshadowing his role as Holmes' future nemesis.