I think you are referring to Book 3. In this chapter, “Knitting Done” all of the dots are connected. Dr. Manette was imprisoned because of the baby he delivered for Charles Darnay’s uncle, the Marquis St. Evremonde. He condemned the Marquis and his whole family for the rape or impregnation of the young woman. This is the reason he has his relapse when Lucie marries Charles, because the connection with the name and the events that sent him to prison is too painful. As the nephew, when his uncle is killed the title of Marquis is passed to Charles, making him, his wife and his daughter nobility. It is now a crime to be noble in France, and Dr. Manette has signed his son-in-law’s death warrant with his letter condemning the St. Evremondes, so Darnay is sentenced to death. Mr. Lorry, as always, plays the role of protector and facilitator of both the story and the family by getting Lucie, Charles and the daughter out of France.