At the book's opening, two men, Mr. Utterson and his cousin Mr. Richard Enfield, are leisurely walking through London. Initially silent, the men pass a mysterious basement cellar door, and Mr. Enfield launches into a story about a strange occurrence related to the door. Late one night, while on his way home, Enfield chanced upon a deformed, short man who trampled a girl in the street on her way to fetch a doctor. The girl's family and Mr. Enfield catch the mysterious man and instead of getting the police, decide to force him to give the girl's family money. Agreeable to this compromise, the mysterious man disappears into the cellar door and returns with a check bearing not his own name, but that of the respectable Dr. Jekyll. Although Enfield assumed the check would be a forgery, it proves to be legitimate.
After hearing the story, Utterson returns to his home where he removes his friend and client Dr. Henry Jekyll's mysterious will, which Jekyll recently filed. The will states that in case of Dr. Jekyll's death, his substantial estate will pass to Mr. Edward Hyde, whom Utterson has never met and whom he assumes is the mysterious man in Enfield's story. Even stranger, the will states that in case of Jekyll's disappearance for more than three months, Hyde will assume Jekyll's estate without delay. Utterson also realizes that the mysterious door is connected, in an L shaped way, to Jekyll's home. Utterson concludes that Hyde is blackmailing Jekyll and resolves to seek the man out to understand why. After tracking the man down, Hyde is initially civil but turns angry when Utterson extends the conversation, probing into his relationship with Dr. Jekyll.
One year later, Edward Hyde brutally murders Sir Danvers Carew by beating him to death with a cane. With help from Utterson, the police find Hyde's apartment ransacked and all papers burned. After leaving, Utterson proceeds to Jekyll's and confronts him for harboring a murder. Jekyll claims that he is done with Hyde forever and that their relationship is terminated. Jekyll does, however, have a farewell note from Hyde. Utterson examines the note and his clerk, Mr. Guest, later discovers that the handwriting, although slightly altered, matches a dinner invitation written by Dr. Jekyll. Angrily, Utterson assumes that Jekyll has forged a letter for a murderer.
More time passes, and we learn that although Hyde has not been located, Dr. Jekyll has become increasingly social, returning to his pre-Hyde days of friendly meetings and intellectual gatherings. One day, Utterson attends a dinner party at Jekyll's home and sees Dr. Lanyon there. Shortly thereafter, Jekyll secludes himself and Dr. Lanyon falls severely ill due to "shock" and dies. After his death, Dr. Lanyon leaves Utterson a letter instructing him only to read it after Dr. Jekyll's death or disappearance. Some time after these mysterious events, Enfield and Utterson again walk by the mysterious door and get a rare glimpse at Dr. Jekyll, who is sitting by a window in the apartment. The men have a brief conversation, but Jekyll abruptly shuts the window as he begins to suffer what appears to be a seizure. Enfield and Utterson are struck by the disturbing appearance of Jekyll's face as he withdraws from view.
About a week later, Richard Poole, Jekyll's faithful butler, approaches Utterson. Poole reports that Jekyll has locked himself in his cabinet and strange sounds, including crying and pacing are all that have been emanating from the room. The only communication that Poole has received from Jekyll consists of letters desperately asking for a specific type of medicine. Utterson agrees to assist and follows Poole to Jekyll's house. The two men break down the door to the room where Jekyll has hidden himself. They find Hyde's dead body and assume he committed suicide immediately before they entered the room. They ransack the area looking for Jekyll's body or evidence of his death, but are unsuccessful. In the laboratory, the men discover a large envelope addressed to Mr. Utterson. Inside, Jekyll urges Utterson to read the package from Lanyon and if he wishes to know more, read the further description Jekyll provides within the envelope.
Utterson reads Lanyon's narrative. The letter begins with a description of a strange letter Lanyon received from Henry Jekyll, the night after a dinner party at Jekyll's residence. The letter urges Lanyon to go to Jekyll's house and fetch a certain drawer with specific contents from the laboratory. Afterwards, a messenger will come to Lanyon's house in Jekyll's stead to recover these items, which include powder, a phial, and a paper book. Lanyon follows the instructions thinking that Jekyll has lost his mind. Mr. Hyde appears at the specified time, looking particularly strange, dressed in clothes far too large for him. Lanyon gives Hyde the ingredients. Hyde then asks Lanyon whether or not he would like to see the end result of his errand. Lanyon is curious and agrees. Hyde mixes the ingredients into a potion, drinks it, and transforms into Dr. Jekyll as an astounded Lanyon observes. Lanyon is deeply affected by this shock and the pure evilness of Jekyll, brings on his subsequent illness and death.
After reading Dr. Lanyon's account, Utterson reads Jekyll's own description of his failed experiment. Jekyll believed that the soul is made up of two separate distinctions: good and evil. These two separate beings live in continuous and inherent conflict with each other. Slowly, Jekyll begins an experiment where he attempts to completely differentiate these two aspects of human nature. Jekyll experiments extensively and then makes two potions. One transforms him into Edward Hyde, and the second transforms him back into Henry Jekyll. This amazingly successful experiment begins Jekyll's extensive exploration of his other self, a man entirely comfortably in morally corrupt behavior, whom he eventually names Edward Hyde.
For some months, this behavior continues until Jekyll, "had gone to bed Henry Jekyll, [and] had awakened Edward Hyde." Jekyll was alarmed that he transformed into Edward Hyde without the assistance of the potion, and became concerned that the character of Hyde might irrevocably take over. Concerned that he had overstepped his bounds, Jekyll chose to give up the freedom of Hyde and for two months maintained the identity of Dr. Jekyll. Unfortunately, he was tortured with Hyde's longing to freely take part in evil doings, and he once again took the potion. During this transformation, Hyde brutally murdered Carew. Because of the manhunt for Hyde, Jekyll swore off ever again making the transformation and set out to try to remedy the evil inside of him.
Unfortunately, at this point Jekyll had given too much power to his evil side. Hyde was an irrevocable part of Jekyll's character, and the many transformations and evil behaviors only strengthened Hyde's power. One night, while contemplating Hyde's deeds, Jekyll spontaneously transformed into Edward Hyde. Because his dual identity was a secret to all members in his house, he realized he could not walk through his house to the laboratory to retrieve the potion's ingredients. Therefore, he sent the urgent letter to Dr. Lanyon. After successfully turning back into Dr. Jekyll, he went home once again but every time he fell asleep, he reverted to Mr. Hyde. Soon, his potions failed to work, even at double strength, and he ran out of the specific medicine needed. While living in the cabinet apartment and not allowing any of his servants to see him, Hyde launches a desperate but unsuccessful search across London for the potion ingredients. When Poole and Utterson finally break into the room, Hyde kills himself, thus finally releasing both Jekyll and Hyde.