While the History concentrates on the military aspects of the Peloponnesian War, it uses these events as a medium to suggest several other themes closely related to the war. It specifically discusses in several passages the socially and culturally degenerative effects of war on humanity itself. The History is especially concerned with the lawlessness and atrocities committed by Greek citizens to each other in the name of one side or another in the war. Some events depicted in the History, such as the Melian dialogue, describe early instances of realpolitik or power politics.
The History is preoccupied with the interplay of justice and power in political and military decision-making. Thucydides' presentation is decidedly ambivalent on this theme. While the History seems to suggest that considerations of justice are artificial and necessarily capitulate to power, it sometimes also shows a significant degree of empathy with those who suffer from the exigencies of the war.