A performer is killed during a bullet catch trick at Buffalo Bill's Wild West show. Although the man's death appears to be a freak accident, Murdoch suspects he may have been murdered and uncovers a dark secret in his past which would provide ample motive. Brackenreid's wife joins the Temperance League and chastises him for his heavy drinking.
When a serial killer begins mutilating and disemboweling women, a tenacious Scotland Yard detective who believes that the killer may be Jack the Ripper inserts himself into Murdoch's investigation. Murdoch calls upon the expertise of an alienist, Doctor Roberts, to help profile the murderer.
Murdoch's investigation takes him inside the cutthroat world of 19th century paleontology when the grand unveiling of a dinosaur skeleton reveals a corpse in the creature's mouth.
Murdoch must solve a seemingly impossible robbery when a thief burgles a sealed bank vault without opening the door. A witness claims to have seen Harry Houdini fleeing the scene of the crime. Meanwhile, Julia's younger sister, Ruby, visits Toronto.
The garroted corpse of a prostitute is discovered after a high-class brothel is firebombed. Murdoch must tread carefully when he discovers that a prominent judge may be to blame. The Temperance League puts pressure on Brackenreid to stamp out prostitution in Toronto. Murdoch and Ogden finally give in to their mutual attraction and begin a romantic relationship.
A young woman's body is found in a creek, and Murdoch's investigation reveals she died of poisoning following an attempted abortion. The case hits close to home for Dr. Ogden, who reveals to Murdoch that she had an illegal abortion some years previously, putting a strain on their relationship.
Murdoch attempts to unravel what appears to be the perfect murder when a gunman shoots a college professor from a crowded plaza, yet is seen by no one. Two eager students, James Gillies and Robert Perry, shadow Murdoch during the investigation. Crabtree reveals himself to be a foundling and attempts to locate his biological mother.
Murdoch investigates the bizarre murder of a mathematics professor. Meanwhile, a young boy's report of a giant silver knight roaming the woods attracts the attention of Terrence Meyers and the Canadian Government, who believe it may be a weaponized automaton. Murdoch begins courting the boy's mother, Enid Jones.
Murdoch is seriously injured while chasing a murder suspect. While recovering, he is confined to his bedsit, but strange noises and increasingly fevered visions lead him to suspect his landlady may be up to something. Crabtree becomes acting detective in Murdoch's absence and takes over the murder case, only to discover that the sole witness is a parrot.
Murdoch learns that Toronto's female telegraphers are falling prey to a predatory conman when one of his marks is murdered. Murdoch's relationship with Enid is strained when he jeopardizes her safety in order to catch the killer. Brackenreid's usage of a cocaine-based gold cure for alcoholism causes him to become increasingly belligerent, further straining his marriage and his relationship with his co-workers.
A young Jewish man who was involved in a love triangle is poisoned. While it initially appears that a jealous suitor is to blame, Murdoch's discovery that the victim's friend is trying to form a union leads him to suspect more sinister motives. Murdoch and Enid's relationship continues to flounder.
Several men who had been on a hunting trip together are stalked and brutally murdered by a creature that appears to be a werewolf. Murdoch and Enid's relationship comes to an end when they both realize he is still in love with Julia.
Murdoch finds a rival in the form of RCMP officer Jasper Linney when they both begin investigating the same murder. The case leads them to British Columbia, where they encounter Murdoch's father. Murdoch rekindles his relationship with Julia.