The threats of the Persian Empire had represented a threat to Greek independence, and by extension, the future of governance through democracy. Likewise, the Peloponnesian War threatened the Greek political system, by ending the polis system of governance.
In the 50 years between The Persian Wars and The Peloponnesian War, the cities of Athens and Sparta were considered ‘first among equals’ among the rest of the Greek city-states. However, human nature being what it is, envy, greed, and fear eventually caused a rivalry to spread. Thucydides, who was present for the conflicts and who wrote a masterful history of the period, believed the eventual war was started by Sparta. He supposed Sparta began to feel trapped by the burgeoning Athenian power. Athens and Sparta were both powerful arenas, especially after the successful conflicts against Persia. At the time, they were both run by Leagues (loose-alliances that were headed by a dominant city-state). Athens had its Delian League, and Sparta had its Peloponnesian League. Unfortunately, the two leagues were the beginning of the end for the Greek polis system.
Originally the Delian League was meant to provide the organizational structure to fight against the Persians; however, Athens began to use the League's navy for its own purposes. Further, minor city-states, in the Delian League, practiced their traditional form of democratic governance, but Athens made the major decisions. This did not sit well with the other members of the League, sparking a variety of minor conflicts. Athens had the powerful and expansive navy, along with other alliances at its disposal, which it continued to grow and develop in case Persia should return.
The Peloponnesian League was organized under more broadly democratic terms, with two council-bodies and with all the member city-states having a vote in one of the councils. Sparta held the most sway, being the only city able to call everyone together, and all the other city-states were made to have alliances with Sparta. They could also have alliances with each other, but they were not required to. Sparta also had an advantage over the other cities in that it could field a standing army of hoplite infantry (citizen soldiers), who were not bound to farmers' fields like the militaries of other city-states would have been. Also, Sparta could call up an additional two hundred thousand soldiers (Helots) from their allies and their own population.
The war between these two powerful forces began with Athens inserting itself into a conflict between Megara and Corinth, both of which were allies of Sparta. Athens was able to secure an alliance with Megara, which gave the Delian League a foothold on the Isthmus of Corinth, with which they could isolate the rest of the Peloponnesus.
Sparta was soon pulled into the conflict, which quickly widened into a greater war. This war is not what many consider the Peloponnesian War, but it functions in much the same way that World War I was the prelude to World War II. Eventually, peace would be found, but peace would be short-lived, and tempers would only smoulder.
This prelude conflict began in 459 BC, with the war between Megara and Corinth, and concluded in early 445 BC. Athens was unprepared for the conflict, and faced with a massive Spartan invasion of Attica; they were willing to accept Sparta's terms: cede lands and allies on the mainland. Both Athens and Sparta were still in control of their respective leagues and alliances. The peaceful resolution lasted only fifteen years.
The provocation that sparked the Peloponnesian War, once again, came down to Athens' relationship with Megara. In approximately 432 BC, following further problems with both Corinth and Megara (which was an ally of Sparta at this time), Athens enacted a trade embargo against the citizens of Megara. This embargo was disastrous for Megara's economy. At the request of Corinth, Sparta called together all members of the Peloponnesian League to Sparta to discuss what to do about the situation. Many of the city-states had grievances against Athens, aside from what was being done to Megara; the assembly voted, and a majority found Athens in violation of the peace. This meant war.
The Peloponnesian League, except for Corinth, were land-based powers which could field mighty armies. Just like the first conflict, Sparta and its allies invaded Attica and drove the Athenians from the countryside. Wisely, the Athens did not try and fight Sparta's vastly more superior force, and instead retreated behind its thick walls.
Furthermore, Athens still held its port and was supported by its more-than-capable navy. The Athenian leader, Pericles, had a plan: rely on the navy to ensure the increased importation of food and material into Athens, while also sending the fleet out to stabilize its coastal allies and prevent infiltrations from Sparta and its allies, all while avoiding major land engagements at any costs.
Sparta relied on a strategy of stealing crops and burning what they could not carry. While this kept their bellies full, the Spartans were unsuccessful in drawing out the Athenian army nor driving the city into capitulation. What eventually tipped the stand-off in the Spartans' favour was an outbreak of plague within the city, which killed Pericles and one-fourth of the citizens. This had given the Spartans the upper hand in the conflict.
However, even though death and disease in that battle, the Athenians were not deterred. With their refusal to surrender, both sides looked to secondary objectives throughout the Aegean, Asia Minor, and Sicily. Also, Sparta sought to turn members of the Delian League, and Athens sowed discord among the Spartan Helots.
In these subsequent conflicts, Athens used its allies' hoplites (citizen soldiers) in maritime operations, while Sparta spent time building a navy. Ultimately, during the Peloponnesian War, there were no more than a few pitched battles among vast armies. This represented a difference from how wars were fought previously, and it resulted in vast swathes of destruction, but no real change for the broader course of the conflict.
The Athenian strategy yielded some gains, primarily with the capture of Pylos in 425 BC. The Spartans, who were defending the city, were captured and there was a brief insurrection among the Helots. Not content with just capturing their enemies, Athens began to attack neutral city-states around the Aegean. This foolish decision was not the last one they made, as the Athenians also embarked on an expedition to Sicily to aid one of their allies against one of Sparta's allies. This resulted in the loss of more than 40 thousand Athenians dying in the fields of Sicily, a thousand miles away from Athens.
Sparta also established a permanent base of operations in Attica at Decelea. This was to further destabilize Athens' allies by encouraging army desertions and disrupting their economies. After the terrible plague and the disastrous foray into Sicily, Athens was unable to replace their manpower losses and soon found both their army and navy routinely outnumbered. Persia, sensing an opportunity to make inroads amongst its enemies, also subsidized Sparta, and its allies.
The Athenians finally faced defeat at a naval confrontation off Aegospotami. Sparta had won. The Long Walls, which were the lifeblood that connected Athens and its port, were burned to the ground. A Spartan force now occupied the city.
Thirty years of fighting in the Aegean, Attica, Peloponnesus, and Sicily left Athens impoverished, demoralized, and depleted. However, it was a poor outcome for both sides. Sparta and its allies were not in any position to maintain a long-term, overarching hold over all of Greece.
The Peloponnesian War had brought an end to the polis system. It had also moved armies away from the traditional way of fighting wars, where farmer-soldiers balanced their time between the battlefields and the wheat fields. Warfare now meant broad conflicts involving naval invasions, long sieges, and scorched earth approaches. Greece was wounded, and soon an invader from the North would change everything once more.