The Reptile Room, a children's novel, is the second installment in A Series of Unfortunate Events. Having just escaped the clutches of evil Count Olaf, the three Baudelaire orphans are sent to live with their Uncle Monty, a friendly man who studies snakes for a living. When Monty's new assistant turns out to be Count Olaf in disguise, the children must figure out a way to warn their Uncle before it's too late.
The three Baudelaire orphans have been placed under the care of their distant relative, herpetologist Dr. Montgomery Montgomery. "Uncle Monty", as he prefers to be called, is a short, chubby man with a round, red face. The children immediately like him. He lets them each choose their own bedroom and informs them that they are going to accompany him on a trip to Peru to study snakes.
The children are fascinated by the many snakes in the "Reptile Room", a giant hall in which Monty's reptile collection is stored. They meet the Incredibly Deadly Viper, a friendly snake with a misleading name which Uncle Monty recently discovered. The three children are each given jobs in the Reptile Room: Violet is given the job of inventing traps for new snakes found in Peru, Klaus is told to read books on snakes to help advise Uncle Monty, and Sunny's job is to bite ropes into usable pieces.
When Stephano, the successor of the original assistant Gustav arrives, the children realize he is Count Olaf in disguise. Count Olaf is a villain who the children used to live with, until he was caught trying to steal the fortune left behind by their parents. They try to warn Uncle Monty, but Stephano threatens them with violence. They manage to talk to Monty alone the day before their trip to Peru, but Monty is convinced that Stephano is a spy trying to steal information from his research and fails to understand their claims that Stephano is Olaf. He tears up Stephano's ticket to Peru. The following morning, the Baudelaires discover Monty's dead body with 2 holes in his neck in the Reptile Room.
Stephano still intends to take the children to Peru, where he aims to find a way to get his hands on their fortune. However, as they are leaving the estate, Stephano's car crashes in Mr. Poe's car. They return to the house, where Poe and Stephano discuss what to do with the children. Mr. Poe refuses to believe the children when they say Stephano is Count Olaf in disguise, as Stephano lacks a tattoo of an eye on his ankle. Dr. Lucafont arrives and performs an autopsy, claiming Monty was killed by the Mamba du Mal.
Violet tells her siblings to cause a distraction, in which they have the Incredibly Deadly Viper to pretend to attack Sunny, while Violet creates a lockpick from the charger of Klaus' reading lamp. She then uses it to open Count Olaf's suitcase to reveal needles with the venom from the Mamba du Mal, as well as some powder that he used to cover up the eye tattoo. Klaus reveals to Mr. Poe, Dr. Lucafont and Count Olaf that, from his studies of the Mamba du Mal, if the Mamba du Mal attacked Uncle Monty he would be almost completely black, while Monty was completely pale. Violet shows her evidence, and Mr. Poe rubs away the powder on Stephano's ankle to reveal the eye tattoo.
Dr. Lucafont is revealed to be one of Count Olaf's henchmen, the hook-handed man, and the 2 criminals escape after revealing that Gustav did not quit but was drowned by Olaf. A man named Bruce comes over to bring the reptiles of the Reptile Room to another company as the children tearfully depart the Incredibly Deadly Viper.