What is the main conflict in The Wine-dark Sea by Patrick O'Brian?

Surprise, a British hired vessel of war, is nominally commanded by Tom Pullings, but in actual fact is commanded by Jack Aubrey. The ship's secret mission is to transport Stephen Maturin, an undercover agent of the British Naval Intelligence service, to Peru where he will use British money and local contacts to foment a rebellion against Spanish rule in favor of local autonomy. The mission must remain very secret because Spain is a theoretical ally of Britain. Surprise voyages across the Pacific Ocean, taking a few prizes and having some exciting adventures, before landing Maturin in Peru. One of the ships captured by Surprise contains a Frenchman named Dutourd. Dutourd is a champion of civil rights and equality and his radical ideas of free society are quite appealing to some crewmembers of Surprise.