In 'Doubting Thomas,' Sherlock enlists the help of Birtwistle, an insurance investigator known for his sharp skills and resourcefulness, to assist in the search for missing jewels linked to the kidnapping of Sherlock's friends. Their partnership introduces a new dynamic as they have different approaches to solving the mystery, leading to intriguing interactions while navigating the case's complexities.

Amelia leaves 221B Baker Street to move into the Anderson residence to serve as Clara's chaperone. During Clara's etiquette training, Amelia encounters clues related to a murder, discovers ties to the organization called The Thread, finds a twin blade similar to the one used to kill her mother, and narrowly escapes an abduction attempt, all within this episode.

The episode explores the links between the missing jewels and the recent kidnapping of Sherlock's friends. Additionally, investigations reveal connections to the insidious organization known as The Thread, with Lady Violet Somerset implicated as having ties to this group, which both Sherlock and Amelia aim to expose.

Sherlock has a significant conversation with young Dan regarding Dan's father and his growing closeness to Amelia. Meanwhile, Sherlock uses his new telephone in unconventional ways to support the investigation, uncovering connections that reinforce Amelia's findings about the villains surrounding them.

Amelia is nearly abducted during the episode, adding tension and danger to the storyline. The episode also features a murder that Amelia witnesses, and the race against time to find the missing jewels linked to the kidnapping heightens the stakes for Sherlock and his allies.