Lee's Dilemma: Conflicted Choices in the Civil War Lee's dilemma during the Civil War revolved around his loyalty to Virginia and the Confederacy versus his moral reservations about slavery and secession. As a distinguished military leader, General Robert E. Lee faced profound conflict when choosing to command the Confederate Army. Though he believed in states' rights, he struggled with the implications of fighting for a cause that upheld slavery. This internal conflict shaped Lee's leadership,