The first book of the History, after a brief review of early Greek history and some programmatic historiographical commentary, seeks to explain why the Peloponnesian War broke out when it did and what its causes were. Except for a few short excursuses (notably 6.54-58 on the Tyrant Slayers), the remainder of the History (books 2 through 8) rigidly maintains its focus on the Peloponnesian War to the exclusion of other topics.
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.
For the most part, the History does not discuss topics such as the art and architecture of Greece.
The History emphasizes the development of military technologies. In several passages (1.14.3, 2.75-76, 7.36.2-3), Thucydides describes in detail various innovations in the conduct of siegeworks or naval warfare. The History places great importance upon naval supremacy, arguing that a modern empire is impossible without a strong navy. He states that this is the result of the development of piracy and coastal settlements in earlier Greece.
Important in this regard was the development, at the beginning of the classical period (c. 500 BC), of the trireme, the supreme naval ship for the next several hundred years. In his emphasis on sea power, Thucydides resembles the modern naval theorist Alfred Thayer Mahan, whose influential work The Influence of Sea Power upon History helped set in motion the naval arms race prior to World War I.
The History explains that the primary cause of the Peloponnesian War was the "growth in power of Athens, and the alarm which this inspired in Sparta" (1.23.6). Thucydides traces the development of Athenian power through the growth of the Athenian empire in the years 479 BC to 432 BC in book one of the History (1.89-118). The legitimacy of the empire is explored in several passages, notably in the speech at 1.73-78, where an anonymous Athenian legation defends the empire on the grounds that it was freely given to the Athenians and not taken by force. The subsequent expansion of the empire is defended by these Athenians, "...the nature of the case first compelled us to advance our empire to its present height; fear being our principal motive, though honor and interest came afterward." (1.75.3)
The Athenians also argue that, "We have done nothing extraordinary, nothing contrary to human nature in accepting an empire when it was offered to us and then in refusing to give it up." (1.76) They claim that anyone in their position would act in the same fashion. The Spartans represent a more traditional, circumspect, and less expansive power. Indeed, the Athenians are nearly destroyed by their greatest act of imperial overreach, the Sicilian expedition, described in books six and seven of the History.
Thucydides correlates, in his description of the 426 BC Malian Gulf tsunami, for the first time in the history of natural science, quakes and waves in terms of cause and effect.