I said there were two things main things to look at in regards to Thucydides, and I wrote about his legacy in terms of how history should be written. The other thing is the war itself. On the dawn of the war, Thucydides judged that it would be a big deal and he wanted to future generations to know about it. What he couldn't have known was just how unusual and complicated a war it would be.
The usual plan for war was for two city-states (or more) to basically declare themselves to be fighting each other. They would then meet on a plain and face off in battle. The winner would exact terms from the loser and that would be that. Athens was a stronger city, but the Spartans (and her allies) were more feared on land. The Athenians were masters of the sea.
Not so here. Pericles, the leading politician of Athens, decided that the walls of the city and adjoining port, were strong enough that if the Spartans came, they would simply shepherd everyone inside and wait until the army went away. Sure enough, the Spartans invaded and everyone who lived and worked in the countryside, sheltered within Athens. The port remained open and the city was fed.
Fed, but not well. An enormous plague occurred, one such as had never been encountered before. It killed tens of thousands. Modern day historians are still arguing over what kind of plague it was but no one really knows. Anyway, the Athenians were sheltered from direct fighting but still dying in large numbers.
Meanwhile, the Athenians came up with some unusual tactics of fighting. They sailed around and attacked various Spartan (and Spartan friendly) ports. Once there, they encouraged the Spartan helots to rebel.
The Peloponnesian war went through hot and cold phases. It stretched on for 30 years, firmly stamping itself on the lives of the Greeks. In Athens, reputations could be lost forever if one didn't act well on the battle field. Fortunes were lost and whole families were wiped out by sickness and war. Eventually, Sparta won and Athens was humbled.