In Chapter I of Book the Third, Dickens writes that after his arrest, Charles Darnay stands
...in a company of the dead, Ghosts all! The ghost of beauty, the ghost of stateliness, the ghost of elegance, the ghost of pride,... all turning on him eyes that were changed by the death they had died in coming there.
Then, in Chapter X of Book the Third, having been released from prison by the testimony of Dr. Manette, Charles Darnay is again arrested. He is condemned for three reasons: He is "[A]t heart and by descent an Aristocrat"; he is "an enemy of the Republic"; he is "a notorious oppressor of the People." All three of these charges are unjust.
1. "At heart and by descent an Aristocrat"
Darnay has changed his name from Evremonde, been renounced by his uncle, and left France. After his uncle's death, Darnay no longer collects any rents on the Evremonde property, having instructed his overseer Gabelle to reliquish all rents.
2. "An enemy of the Republic" as an emigrant
Darnay is condemned based upon a decree which banished all emigrants on pain of Death that is dated since his return to France, so he is not "an emigrant" or enemy of the Republic.
3. "A notorious oppressor of the People"
Darnay has lived in England for years; therefore, he has oppressed no one in France. He has been written in the "fatal register" of Saint-Antoine only because he is the son of the Evremonde brothers who injured the family of Madame Defarge. She tells her husband why Darnay must be condemned because the mortally wounded boy that Dr. Manette treated was her brother, that sister of this boy was her sister, and the father her father,
"...those dead are my dead, and that summons to answer for those things descends to me!"