There are numerous external conflicts in the story; it is set during the Revolutionary War, after all. But the most important conflicts are the internal conflicts within Jonathan himself. These take on many different forms as the story progresses. At the start of the book, Jonathan regards war as an awfully big adventure, a chance to prove his manhood and gain a reputation as a hero. But fairly soon after he sets foot on the battlefield, Jonathan becomes thoroughly disillusioned. War is a truly horrifying experience, full of death, suffering, and bloodshed. Jonathan is forced to grow up pretty quickly and cast aside his boyish enthusiasm for war.
Jonathan has been steeped in the revolutionary tradition almost since he could walk. He is as much of a patriot as anyone. But once again, he finds himself conflicted inside by his experiences on the battlefield. The Hessians are supposed to be the enemy, but they treat Jonathan decently after they capture him. By the same token, he also finds that many on his own side act more barbarically than the so-called enemy. Jonathan's experiences make him conflicted in his loyalties. On one hand, he is still an American patriot, but on the other, he now realizes that all human beings are unique and that the black-and-white picture of the conflict painted by revolutionary propaganda does not begin to tell the whole story.