Gabriel John Utterson and his cousin Richard Enfield reach the door of a large house on their weekly walk. Enfield tells Utterson that months ago he saw a sinister-looking man named Edward Hyde trample a young girl after accidentally bumping into her. Enfield forced Hyde to pay £100 to avoid a scandal. Hyde brought them to this door and provided a cheque signed by a reputable gentleman (later revealed to be Doctor Henry Jekyll, a friend and client of Utterson). Utterson is disturbed because Jekyll recently changed his will to make Hyde the sole beneficiary. Utterson fears that Hyde is blackmailing Jekyll. When Utterson tries to discuss Hyde with Jekyll, Jekyll tells Utterson he can be rid of Hyde when he wants and for Utterson to drop the matter.
One night in October, a servant sees Hyde beat Sir Danvers Carew, another one of Utterson's clients, to death. The police contact Utterson, who leads officers to Hyde's apartment. Hyde has vanished, but they find half of a broken cane (the other half having been left at the crime scene). Utterson recognizes the cane as one he had given to Jekyll. Utterson visits Jekyll, who shows Utterson a note, allegedly written to Jekyll by Hyde, apologising for the trouble that he has caused. However, Hyde's handwriting is similar to Jekyll's own, leading Utterson to conclude that Jekyll forged the note to protect Hyde.
For two months, Jekyll reverts to his former sociable manner, but in early January, he starts refusing visitors. Dr Hastie Lanyon, a mutual acquaintance of Jekyll and Utterson, dies of shock after receiving information relating to Jekyll. Before his death, Lanyon gives Utterson a letter to be opened after Jekyll's death or disappearance. In late February, during another walk with Enfield, Utterson starts a conversation with Jekyll at a window of his laboratory. Jekyll suddenly slams the window and disappears.
In early March, Jekyll's butler, Mr. Poole, visits Utterson and says Jekyll has secluded himself in his laboratory for weeks. Utterson and Poole break into the laboratory, where they find Hyde wearing Jekyll's clothes and apparently dead from suicide. They find a letter from Jekyll to Utterson. Utterson reads Lanyon's letter, then Jekyll's. Lanyon's letter reveals his deterioration resulted from the shock of seeing Hyde drink a serum that turned him into Jekyll. Jekyll's letter explains that he had indulged in unstated vices and feared discovery. He found a way to transform himself and thereby indulge his vices without fear of detection. Jekyll's transformed body, Hyde, was evil, self-indulgent, and uncaring to anyone but himself. Initially, Jekyll controlled the transformations with the serum, but one night in August, he became Hyde involuntarily in his sleep.
Jekyll resolved to cease becoming Hyde. One night, he had a moment of weakness and drank the serum. Hyde, his desires having been caged for so long, killed Carew. Horrified, Jekyll tried more adamantly to stop the transformations. Then, in early January, he transformed involuntarily while awake. Far from his laboratory and hunted by the police as a murderer, Hyde needed help to avoid capture. He wrote to Lanyon (in Jekyll's hand), asking his friend to bring chemicals from his laboratory. In Lanyon's presence, Hyde mixed the chemicals, drank the serum, and transformed into Jekyll. The shock of the sight instigated Lanyon's deterioration and death. Meanwhile, Jekyll's involuntary transformations increased in frequency and required ever larger doses of serum to reverse. It was one of these transformations that caused Jekyll to slam his window shut on Enfield and Utterson.
Eventually, one of the chemicals used in the serum ran low, and subsequent batches prepared from new stocks failed to work. Jekyll speculated that one of the original ingredients must have some unknown impurity that made it work. Realizing that he would stay transformed as Hyde, Jekyll decided to write his "confession". He ended the letter by writing this: "Here then, as I lay down the pen and proceed to seal up my confession, I bring the life of that unhappy Henry Jekyll to an end." With these words, both the document and the novella come to a close.