Charles Darnay, one of the main characters of A Tale of Two Cities, is arrested three times in the course of the novel, each time on a different charge. He is first arrested in 1780, as a French emigre in Great Britain, for treason against the British Crown, after being falsely accused of having sold information about British troops to the French by a pair of British spies.

After returning to his native France in 1792 at the height of the Reign of Terror to attempt to free a former servant of his family, he is arrested for the second time for the crime of being an emigrant aristocrat, and incarcerated in La Force prison.

Although he is quickly released following the intercession of his father-in-law, Dr. Alexander Manette, he is soon arrested for the third time after Madame Defarge reveals that he is the nephew and heir of the wicked Marquis St. Evremonde. Unbeknownst to Charles, his uncle and father had kidnapped and raped the pregnant sister of Madame Defarge, resulting in her death and that of her child. 

The second time Darnay is arrested for being an emigrant he is imprisoned only briefly. Dr. Manette uses he influence to free Darnay. Yet almost immediately upon being released he is arrested again based on charges from the DeFarges and "one other." This final arrest sets in motion the exchange between Carton and Darnay that leads to the novel's climax.

The first time Darnay is arrested, it is because he has been accused of conducting secret business between France and England for at least five years; in other words, he is accused of being a spy.

The second time he is arrested, he is on his way to Paris; Darnay is captured, imprisoned, charged with being an aristocratic emigrant. Now he must suffer the justice of the revolution.

Why was Dr. Manette arrested in the book Tale of Two Cities?

Dr. Alexandre Manette was arrested on false charges after being lured from his home. The purpose of the arrest was to remove him from society in order to prevent his speaking out against the Evrémonde brothers and their heinous actions.

After Charles Darnay has been arrested and denounced by Madame Defarge and others in Chapter 10 of Book the Third, Ernest Defarge produces as evidence against Charles a paper that he found in Dr. Manette's cell in the Bastille. Dr. Manette's letter is then read as evidence against the Evrémondes, to whose family Charles actually belongs. (He has changed his name.) The contents reveal that Dr. Manette, a highly regarded physician, was brought to a "solitary house" by two armed men who called at his home. They brought him to this dwelling so he could provide medical attention to two peasants who lived on their land, a handsome young man and a beautiful young woman. 

Dr. Manette was initially told that the young man forced one of the gentlemen to draw his sword against him. However, the physician later learned from the young man, who lay dying from a wound inflicted by the gentleman's sword, that he attempted to defend the honor of his sister when one of the two aristocrats tried to sexually assault her. Dr. Manette did what he could for the peasants, but the young man soon died. His sister lasted another night and day before she too died.

Afterward, the elder brother moved a chair near Dr. Manette's. He then told the physician,

"Doctor, finding my brother in this difficulty with these hinds, I recommended that your aid should be invited. Your reputation is high, and, as a young man with your fortune to make, you are probably mindful of your interest. The things that you see here, are things to be seen, and not spoken of." (Bk. III, Ch.10)

Although greatly troubled, Dr. Manette responded,

"Monsieur,...in my profession, the communications of patients are always received in confidence." (Bk. III, Ch.10)

The brothers offered Manette a rouleau of gold, but he refused it. The next morning this rouleau of gold was left at Manette's door in a small box with his name written on upon it.

Manette's letter continues,

"I decided, that day, to write privately to the Minister, stating the nature of the two cases to which I had been summoned, and the place to which I had gone."

Although Manette "knew what Court influence was, and what the immunities of the Nobles were," he still wanted to relieve his own mind. Afterward, he told no one about his experience, not even his wife. Later on that day, he was visited by a young woman who introduced herself as the wife of the Marquis St. Evrémonde. She expressed great concern that the deaths she had learned about would bring misfortune and the "wrath of Heaven" upon the Evrémondes. For the sake of her son and to help the poor family in any way that she could, she expressed a desire to make amends.

After this conversation, Dr. Manette made no mention of the Evrémonde name. He sealed the letter and delivered it himself that day. That night, Dr. Manette was called to Rue St. Honoré by a man in "black dress" who followed Manette's servant into the room where the physician was, forcibly taking him. Once Dr. Manette was far enough from his home, he was gagged and his hands tied. The two aristocratic brothers emerged; one held Manette's letter. This letter was then burned before the physician, and he was subsequently carried off to his "living grave" in the Bastille. 

Why was Dr. Manette arrested in the book Tale of Two Cities?

Dr. Manette was arrested for speaking out about the crimes and injustices perpetrated by the noble Evremonde brothers.

When Dr. Manette was a "young physician, originally an expert surgeon, who...(had) made a rising reputation in Paris", he was commandeered one evening by two noblemen and taken in secrecy to treat two patients.  One was a beautiful young woman with "a high fever of the brain", lying bound on a bed, and the other was her brother, a young man with a mortal wound from a sword thrust.  With his dying breath, the young man told Dr. Manette that he and his sister were peasants who had long lived under the ruthless oppression of the Evremonde brothers.  One of the brothers had become enamored by the beautiful sister and wanted her for his bed; he cruelly worked her husband to death in hopes he would influence his wife to give Evremonde her favors.  The woman's brother had come to avenge her, and was laid low by the sword of Evremonde.

Both patients died, and the brothers Evremonde, chillingly nonchalant and seemingly incapable of sympathy, swore Dr. Manette to secrecy.  The Doctor, however, was troubled, and wrote a letter to to Courts exposing the Evremondes' outrages against the peasant family.  The letter was intercepted;  Dr. Manette was abducted in the night, and put into prison for eighteen years (Book III, Chapter 10).