Episode 2 of "Young Sherlock" begins with Sherlock being arrested for the murder of Professor Thompson.** The officer informs him that there is evidence pointing to his guilt, but Sherlock denies it. He makes a veiled reference to his mother, claiming that he is as deranged as she is. The cop suggests that Sherlock planted the bomb to redeem himself, but Professor Thompson saw him, which forced his hand. Sherlock denies the accusation and asks the officer to speak with Shou'an. He is locked up in prison while Mycroft tries to convince Sir Hodge of Sherlock's innocence.
Sir Hodge tells Mycroft that he benefits from keeping Sherlock locked up and asks Mycroft to stop meddling before leaving. As Sir Hodge runs into James, he brings up the stolen scrolls, claiming that James is not innocent and suggesting that he leave Oxford. James gets upset and lashes out at Shou'an. He packs his bags and leaves the campus, ending up at a costume store.
Meanwhile, Mycroft meets Sherlock in prison and reveals to his brother that Sir Hodge was conspiring to keep him locked up. Sherlock asks his brother to keep this from their mother and discusses Shou'an with Mycroft.
At the same time, Shou'an tells Sir Hodge that she was not with Sherlock on the night of Professor Thompson's murder. Sir Hodge is less concerned about the murder and brings up his trade partnership with Shou'an's father. When Shou'an drops some tea, he goes outside to call Edie to clean up the mess. She leaves the office as Sir Hodge sends a telegram to Mr. Sidney Bluitt, the Minister for War.
James disguises himself as a washerwoman to help Sherlock escape from prison. Mycroft learns about Sherlock's escape and becomes concerned, agreeing to help look for him but warning the cops not to cause any harm.
James asks Sherlock what happened while teaching him how to block a punch. Sherlock reveals how he passed out after having a drink with Shou'an. James concludes that Sherlock was drugged, which explains why he has no memory of the night. He wonders if Shou'an was the one who hid the scrolls and planted the bomb.
The two men disguise themselves as cops to investigate the case further, while Shou'an meets an associate in church, talking to him about Sherlock's arrest. Shou'an tells the man that she can control Sherlock, mentioning how the first apostle has been eliminated.
The man requests Shou’an to track down Professor Roberts, the next target on their list. A flashback reveals Shou’an distracting Sir Hodge and uncovering the names of the four apostles working under him. In parallel, Sherlock and James disguise themselves as constables and sneak into Shou’an’s lodge, seeking clues about her involvement in Professor Thompson’s murder. When Sherlock spots a burning document in the fireplace, Shou’an springs into action, leading to a fierce fight between the two. However, Sherlock manages to escape from Shou’an’s lodge and steps outside.
Meanwhile, Mycroft visits his mother at the mental asylum with Detective Fitget and Constable Vestrade. While Mycroft converses with his mother, the two cops meet the facility's director to determine if Sherlock visited Mrs. Holmes. Mycroft assures Fitget of Sherlock’s innocence.
Sherlock shares his encounter with Shou’an with James and recalls seeing a piece of paper in the fireplace. The two men decode the inscription on the paper and realize that Shou’an had burned a photograph taken by the Oxford Photographers, Lord and Kingsley. James urges Sherlock to visit the photographer to uncover what was in the photo.
Shou’an follows a porter who is delivering essays to Professor Roberts’ house. Sherlock and James take turns distracting the photographer and learn that, besides Shou’an, the Master of the Lodge also possesses a copy of the photograph.
James disguises himself as a constable and sneaks into the lodge. He discovers a photograph of the four apostles listed in Shou’an’s kill list, framed on the wall.
James returns to Sherlock’s lodge and shares his findings. The two men recall seeing the four professors seated at the same table at Sir Hodge’s party. Sherlock concludes that Shou’an is attempting to eliminate all four men who were sitting closest to the fireplace where the bomb was placed.
They ponder what Shou’an was after when Sherlock recalls the names of the four targets: Professor Roberts, an engineer; Enright, a meteorologist; and Mallik, a geologist.
James rushes to speak with the three professors but realizes they are not in their offices. The porter overhears their conversation and informs them about his previous visit to Professor Roberts’ house.
By the time they arrive at the professor's house, Shou’an has already killed Professor Roberts by drugging and choking him. Sherlock feels powerless, but James urges him to try and prevent Shou’an from killing the remaining two professors.
