Amelia goes undercover at Clara Anderson's home to search for clues related to Clara's kidnapping and the stolen jewels, acting as Sherlock's agent where he cannot investigate directly.

Sherlock goes undercover in Newgate Prison by exchanging clothes with Professor James Moriarty, allowing him to meet Charlie, a key suspect, in prison without being recognized.

The red thread is linked to the knife used to stab Amelia's mother, Lucia Rojas, and connects to a larger criminal organization involved in both Clara's kidnapping and Lucia's murder.

Sherlock and Moriarty, former enemies, agree to work together to expose the mysterious crime syndicate known as the 'red thread' organization that has taken over Moriarty's criminal business.

Clara was in love with Charlie, and together they stole her mother's jewels to run away and get married because her parents would never have accepted their relationship. Charlie rushed their plan because he was in danger.