The title of Chapter 1 in Book Three is "In Secret." This chapter takes place in 1792, as Charles Darnay is traveling through France en route to Paris to clear his name. When he awakens in a country inn, he is taken prisoner by patriots and taken to Paris, where an authority decides he will be placed in a prison called La Force. The patriots refer to Darnay as Evremonde. The authority who jails him writes "in secret" on a card and hands it over to Monsieur Defarge, who will accompany Darnay to the prison. This card will be handed to Darnay's jailor once Darnay reaches La Force. "In secret" means that Darnay will have no ability to communicate with the outside world when he is in prison; he will essentially be kept in solitary confinement, and no one in the outside world will know where he is. As he's being taken to prison, Darnay asks Defarge if he will be able to communicate with the outside world, and Defarge refuses to answer.
Although we are never specifically told what it means to be kept "in secret," we can infer what it must be by looking at what happens to Charles Darnay in Book the Third, Chapter 1. Darnay is taken through the general populace of prisoners, who sympathize with him for his sentence of being kept "in secret," assuring him that others have had the same misfortune, and that it is generally not for long. It appears that "in secret" refers to an extreme kind of solitary confinement. Darnay is taken past the regular prisoners, up forty stairs to a cold, dark, solitary cell measuring only five paces by four-and-a-half. Here he is not to be allowed to have paper and pen, only food. There is nothing for him to do but pace the room and try to keep from going mad like his father-in-law Dr. Manette, who, when in prison, "made shoes."