Murdoch has been wrongfully imprisoned for the murder of a burlesque dancer, Julia has been kidnapped, Brackenreid is missing, Constables Jackson and Crabtree have ostensibly been killed and Station House Four has fallen under the thumb of a corrupt city councillor. Murdoch's few remaining allies are forced underground as they work to set things right.
A wine connoisseur is poisoned at his son's wedding after threatening to expose a fraud within the burgeoning Canadian winemaking industry. Detective Watts takes the opportunity to introduce the teetotal Murdoch to the world of wine tasting. Meanwhile, Miss James faces racial discrimination while applying for a job.
A man is murdered at a dark dining event in honour of Helen Keller. Alexander Graham Bell, also in attendance, has secretly made an audio recording of the entire dinner, and the sound of eight mysterious footsteps on the recording is the only clue Murdoch has to work with.
A patient dies on the operating table during a public demonstration of a dangerous and controversial new procedure – an organ transplant. Refusing to accept the consensus that he botched the operation, the lead surgeon becomes convinced that his equipment was sabotaged and turns to Murdoch for help.
Julia's mentor, William Osler, makes the papers when his tongue-in-cheek suggestion that all men over the age of sixty should be euthanized with chloroform is printed as fact. Despite initially dismissing the reports as sensationalist nonsense, Osler's words soon come back to haunt him when a killer starts chloroforming elderly men.
When the sons of an Indian emissary disappear from their boarding school, Murdoch's investigation is hampered by their uncooperative classmates. Hoping to get inside information, he sends Constables Brackenreid and Crabtree undercover.
A traffic collision results in Dilton Dilbert (David Hewlett) being pinned between a carriage and a motor car, and medical investigation reveals that any attempt to free him will result in his death. Evidence that the car has been sabotaged leads Murdoch to suspect that the crash may not have been an accident, and he sets out to uncover the truth as Brackenreid comforts the dying Dilbert.
Murdoch and Ogden stumble across the corpse of an amateur painter while camping. The fellow members of his painting club, who were camped near the crime scene, prove unhelpful. Hoping to find the murderer, Brackenreid goes undercover and rediscovers his talent for art, gaining the attention of a fickle patron who has him paint her in the nude.
A series of obituaries are published for a group of seemingly unrelated people, all of whom are still alive. Among the list is Detective Watts. When a murderer starts killing the people named in the obituaries, Murdoch and Watts scramble to find the killer before they strike again.
James Pendrick returns to Toronto, seeking investors for his newest invention, a high-speed vactrain. When one of Pendrick's employees is killed, Murdoch suspects that he may have been a spy engaging in industrial espionage for the steamship industry.
An amateur cricketer is killed by an exploding bat during the annual "gentlemen vs professionals" match, and Murdoch suspects an exiled Serbian Count may have been the intended victim. During the investigation, Brackenreid and Murdoch get a glimpse into Higgins' new-found upper class lifestyle.
A statue of the Virgin Mary at Murdoch's local church starts weeping blood. The subsequent discovery of an infant's skeleton buried in the churchyard and the apparent suicide of a parishioner lead Murdoch and Watts to suspect the miracle may have been staged in order to bring a long-hidden crime to light. Julia is unsettled by Miss Hart's lack of sympathy in the morgue, and becomes even more concerned when she lies to Murdoch about her faith.
When an acerbic cooking contest judge contracts botulism after eating tainted meat, Murdoch must determine whether the man was intentionally poisoned. Crabtree fears for his life when it emerges that both he and Margaret Brackenreid have also eaten the suspect meat.
Theodore Roosevelt sneaks into Canada to hunt a fabled white moose. Terrence Meyers enlists Murdoch's help in solving a seemingly unrelated locked room murder, but Murdoch soon uncovers a bizarre plot to assassinate the American president, which seems to be spearheaded by a legendary Spanish assassin, El Noche.
A Jewish man is murdered at a Yiddish theatre fundraiser, during a performance by the Jolson Brothers. During the investigation, Watts learns of his Jewish heritage.
Tensions flare between Russian and Polish chess players at a tournament when a Russian master is murdered by someone dressed as a Polish hussar. Crabtree and Nina Bloom go undercover, and discover that the murder may be related to Szczerbiec, a Polish Crown Jewel that was believed to be in the possession of the Russian Empire.
Murdoch and Ogden's relationship crumbles when Julia suffers a miscarriage and William's past misgivings about Julia's prior abortion resurface. The grieving couple are immediately pulled back into work when Nate Desmond is accused of the murder of a man he was seen fighting with.
Believing his relationship to be irreparably damaged, Murdoch avoids facing his issues by skipping work and helping a barfly track down his estranged wife, leaving Watts to investigate the discovery of a limbless torso. Violet Hart colludes with Inspector McWorthy to have Julia ousted from her job on the grounds that her miscarriage has left her unable to perform her duties. Crabtree is forced to accept that he and Nina want different things from life when she accepts a job in Paris; unable to r