I would think the biggest ironic feature in these chapters comes in Chapter Six, entitled "Hundreds of People," and the way that a story is told by Darnay about a hidden prison cell was discovered in the Tower of London by some workmen. They find the cell covered with carvings by prisoners, of "dates, names, complaints and prayers." However, on one corner they see the word "DIG." Note what they did in response to this:
The floor was examined vary carefully under the inscription, and, in the earth beneath a stone, or tile, or some fragment of paving, were found the ashes of a paper, mingled with the ashes of a small leathern case or bag. What the unknown prisoner had written will never be read, but he had written something, and hidden it away to keep it from the goaler.
Note how this mysterious story makes Dr. Manette suddenly become ill, standing up with his hand to his head. It is clear that this story has triggered some deeply repressed memory of his own incarceration, and it is later on in the novel that we discover that Dr. Manette himself wrote such a letter during his incarceration and hid it in his prison cell in the Bastille. It is highly ironic therefore that this story, told by Darnay to Dr. Manette, should mimic what Dr. Manette himself did, and is later used to incriminate Darnay himself.