There were actually three trials through which Charles Darnay went: 1 in England (a trumped-up charge of being a French spy), 2 in France (both were basically for being an enemy of France - an enemy of the state, an enemy of the people, an enemy of the Revolution - since he was a part of the aristocracy).
The reason he is arrested and put on trial again in France is because of the Defarges. They produce a letter, after the trial in which he was freed, bringing evidence against the name of Evremonde. Charles Darnay's family (Evremonde) - the uncle who was murdered, included - had destroyed Madame Defarge's family years earlier. Dr. Manette had gone to prison because of what the Evremondes did, and he wrote an account of what had happened. In that account, Dr. Manette had condemned everyone of the name of Evremonde.
For more information, check http://education.yahoo.com/homework_help/cliffsnotes/a_tale_of_two_cities/4.html;_ylt=AqVJLT8iddWVXhypJM62Gy0ZvskF Yahoo Education - which has a lot of great data on A Tale of Two Cities.
I hope this helps.
