Silas lures Beatrice into a web of deceit, telling her that Cordelia had her institutionalized as a baby and that he, Silas, was the one who rescued her and sent her to live with Mrs. Tilcott. He poisons Beatrice's thoughts against her mother and brothers, keeping her by his side as his protégé, aiding him in his smuggling endeavors.
Years later, Silas learns that Mycroft is working for the government in Oxford. He enlists Beatrice to work for Sir Hodge as his spy. Beatrice informs Silas about the Four Apostles who are working with Sir Hodge and suggests approaching Professor Malik, whom she believes is greedy enough to collaborate with him.
In the present day, Silas continues to manipulate Beatrice with his gaslighting tactics. Sherlock and Cordelia try to defend themselves, but Beatrice believes Silas and stands by his side. At dinner, Silas reminds Sherlock that he needs to bring Shou'an to him in exchange for his freedom. James talks to Beatrice about her disguise as Edie, while Silas tells Cordelia that Beatrice is free to leave if she wishes. The Holmes family tries to convince Beatrice to choose one parent over the other, leading to a heated family argument while James watches on.
Mycroft informs Silas that the British government is willing to purchase the weapon he is creating. This revelation leaves Sherlock and Cordelia feeling betrayed by Mycroft, who was not in Constantinople to have Silas arrested for creating the weapon but was instead trying to negotiate a business deal with him.
James and Beatrice hook up while Silas talks to Sherlock in private. He calls Sherlock his true protégé and agrees to let Beatrice go if Sherlock joins forces with him.
The next morning, Silas dispatches Mycroft to the telegrapher to send a message to the British government. Instead, Mycroft swiftly attacks the guard and sets off in search of Shou’an, who is hiding with Emine. Concurrently, Silas and Beatrice leave for the factory.
As they advance, Mycroft, Shou’an, and Emine converge on Silas’ guards and join forces with Cordelia, Sherlock, and James, who are already engaged in a fierce battle against the guards from within. Once the guards are neutralized, the group investigates Silas’ study.
Inside the study, Sherlock and James uncover a hidden passage that reveals Silas has been using textiles and other trade goods to smuggle a deadly drug. They also learn that Silas and Professor Malik are collaborating on a rocket formula capable of dropping the poison over unsuspecting lands, posing a grave threat to humanity.
Sherlock decodes the equation used to develop the poison and surmises that an antidote might be feasible. James notes that they will require the complete equation to create the antidote. Cordelia discovers a map pointing to the location of the factory, and Emine arranges the horses so that the group can swiftly leave for the factory.
On their way to the factory, Beatrice begins to question Silas and doubt his intentions. He attempts to further manipulate her by urging her not to trust Cordelia. During the journey, James asks Sherlock if he would consider selling the poison formula to the British government for a hefty profit. However, Sherlock is unmoved by this suggestion, and James quickly clarifies that he was only joking as they continue toward the factory.
At the factory, Beatrice muses whether they should consider selling the poison to private individuals rather than limiting themselves to governments. Just then, Sherlock and the rest of the group arrive. Shou’an goes after Professor Malik and kills him. Emine and James follow her lead. Shou’an insists that they must destroy the factory before more lives are lost. The women use the chemicals there to create an explosive device, while James searches for the remaining parts of the formula.
While Cordelia, Mycroft, and Sherlock meet privately with Beatrice, Cordelia brings up an incident from Beatrice's childhood, reminding her of the good times they shared before she was taken away. Gradually, Beatrice realizes that Cordelia was indeed telling the truth. She confronts Silas and fatally shoots him. However, at the same time, Shou'an sets fire to the factory, allowing Silas to escape through the chaos.
Sherlock, Mycroft, Cordelia, and Beatrice manage to get outside as James runs out with the formula alongside Shou'an and Emine. Shou'an chases after Silas, who is attempting to escape on horseback. Sherlock and Beatrice follow them, and the four eventually end up on a cliff.
Shou'an and Beatrice try to kill Silas, but Sherlock stops them. Silas attempts to jump off the cliff with Sherlock but trips instead. He falls off the cliff and dies, leaving Sherlock shocked.
Sherlock looks at Silas's honeycomb print handkerchief that he left in his hand before falling off the cliff. Thinking about his father's final words, Sherlock later discovers a key hidden inside a novel by Charles Darwin. Mycroft asks Sherlock to let go of the key, which he reluctantly does.
Sherlock says goodbye to Shou'an, who leaves to return to China now that she has avenged her people. James and Beatrice meet at a restaurant to discuss Professor Malik's equation for the poison, but he asks her to leave when Sherlock arrives.
Sherlock and James raise a toast to their chaotic personal and family lives. Sherlock tells James that he knows he has the equation for the poison, and James asks Sherlock to work with him.
Sherlock, still skeptical of James's intentions, shows him the key that Silas hid inside the novel. The season ends with Shou'an returning to China, where she reunites with her friends.
