The Beekeeper's Apprentice by Laurie R. King is the story of how a young girl becomes the apprentice to the great Sherlock Holmes. She is so engrossed in the book she is reading that she falls over him while out walking. Though at first she comes across as sassy and argumentative, Holmes immediately sees through her veneer. He recognizes that at long last, after he had given up entirely, he has finally found a person worthy of training as his apprentice. The knowledge that he has finally found someone who challenges and understands his analytical mind is invigorating and instills new life in the super sleuth who had retired to Sussex Downs and become cocaine dependent. With the challenge of mentoring young Mary, he finds new enthusiasm for life.

Holmes begins by challenging Mary with puzzles of all kinds. When he is not testing her mind with puzzles, they play chess or work in his laboratory. He rapidly becomes the father Mary lost in an accident several years previously, and Mrs. Hudson who is Sherlock's housekeeper and companion fills in the large hole that Mary's mother left when she died. Slowly, they heal each other. Mary thrives under the tutelage of Holmes and the nurturing of Mrs. Hudson in all other matters, and Sherlock comes back to life with Mary's company. The tests he devises become ever more challenging, and Mary's powers of deduction and observation grow stronger all the time. Finally, Holmes brings her in on a new case. Together, they solve the mystery surrounding the client and discover that her husband is not the traitor she feared he might be, arresting the man responsible. The thrill of solving the case invigorates Mary. When the manager of her farm tells her about a local robbery at the Inn, Mary becomes involved, but Holmes seems disinterested, telling her to go ahead but leave him out of it. His motivation however is more to give her the confidence to go forward on her own, and she does. Solving this case is tantamount to an addiction in the high it gives Mary and Holmes, though available if needed, is proud of her achievement.

Mary is accepted to Oxford and her life becomes divided. Part of the time, she is a diligent and intelligent student, studying and enriching her mind, and when the breaks between sessions occur, she returns to Holmes where she feels most at home. When the attempts on Sherlock's life begin, Mary realizes for the first time that the work they do can be dangerous as well. In an attempt to get to the bottom of his antagonist, he and Mary use disguises to travel, leave London for several weeks while Mycroft Holmes and Inspector Lestrade attempt to unravel the identity of the mastermind, and in the weeks that follow Holmes and Mary solve yet another case. This time, they must appear to be adversaries themselves. It is a difficult ruse that has Mary doubting herself at times, but the game of cat and mouse works. The evidence leads Mary to realize that their adversary is actually her Math tutor, Miss Donleavy. Donleavy is the daughter of the long dead adversary of Holmes, Moriarty. In a final showdown, Donleavy confronts Mary and Holmes in his laboratory taking them by surprise. At gunpoint, she demands that Holmes sign a suicide note, promising Mary's freedom in return, despite having shot her in the arm already once. When Mary uses an opening to tackle Donleavy, she is shot a second time, but the bullet goes through her shoulder and into Donleavy's heart, killing her. Sherlock is uninjured, and stays by Mary's side until she heals, taking her to his home for convalescence.