The renewal of the war in 415 which ended with the fall of Athens in 404 was a continuation of the Archidamian war of 431-421 but whereas the ideals of 'liberation of the Greeks' on the one side as against the rights of empire on the other were held to be the reasons for conflict, the second war would prove that attitudes had hardened and the opposition become fiercer and the distinction of oligarch v democracy sharpened.The wealthier oligarchic minded citizens of Athens, taking advantage of more moderate discontents, begin to build support for a new constitution. Alcibiades negotiates with the Athenian officers on Samos, promising that he could secure an alliance for Athens with Tissaphernes a Persian satrap, but that dissolution of the democracy would be a condition. Back at Athens, it was voted to move ahead with the negotiations but it became clear that Alcibiades had promised more than he could deliver.
There is some differences between Sparta and Tissaphernes over the extent of Persian rights, but Tissaphernes is still is not ready to break with them in favour of Athens. He proposed impossible conditions for Athens, and renegotiated the treaty with Sparta to limit Persia's claims to Asia.
The coup goes ahead anyway, and in June a council of 400 essentially replaces the Athenian assembly. The Athenian democrats on Samos lead a counter-revolution, establishing government-in-exile, which recalls Alcibiades and elects him general, in the forlorn hope of gaining an alliance with Tissaphernes. Tissaphernes' strategy in 411 is to prolong the war and to take advantage of their conflict to win back the Greek cities and islands that once belonged to Persia.
Meanwhile, there is dissension among the ranks of the 400 who send envoys to Sparta to negotiate a peace. They garrisoned the entrance to the great harbour at Piraeus to be able to admit the Spartans and/or keep out the Athenian fleet from Samos. Negotiations with Sparta fail, and when the Spartan fleet is seen operating in the Saronic gulf, support for the 400 decays, popular uprising against the Pireaus garrison negotiations with the 400 A Spartan fleet of 42 ships appears off Salamis sails around Attica toward Euboea. There an Athenian fleet of 36 ships is utterly defeated. Euboea now revolts. The situation at Athens seems desperate there is no reserve fleet, the army and fleet at Samos is hostile and the main source of supplies has been lost. The Oligarchs are deposed, most of them escape to Decelea, one betrayed Oinoe to the Spartans. A new constitution is put in place.
At the invitation of Pharnabazus a Peloponnesian fleet of 86 ships sailed for the Hellespont followed by an Athenians fleet with 76 ships. At Cynossema a naval battle is fought. The Athenians are extended along the shore of Chersonese, the Peloponnesians planned to outflank the line to prevent it from escaping the straits, and to press the centre in to the shore. Athenians countered by extending their right wing, thus weakening the line. The Peloponnesians were victorious in the centre, but the right wing took advantage of the disorder and threw the Peloponnesian ships into a panic. The Athenian left engaged around the cape of Cynossema, out of sight of the rest of the battle and repulsed Peloponnesians. This was an encouraging victory for the Athenians which was followed by the recovery of Cyzicus, which had revolted.
The period 410 to 406 BC was one of almost continuous naval activity in the eastern Aegean and Hellespont. Pharnabazus the Persian satrap is more actively supporting the Peloponnesians by offering subsidies to pay for crews and troops. The Spartan admiral Mindarus besieges Cyzicus, with the support of Pharnabazus' army. However an Athenian fleet of 86 ships passes into the Hellespont unseen, and takes Mindarus by surprise. Mindarus is killed, and 60 ships taken or destroyed, reducing the Peloponnesian navy dramatically. With its fleet essentially gone, Sparta makes a proposal for peace on the basis of the status quo but Athens is unwilling to abandon an attempt to restore its power in the Aegean and the peace offer is rejected.
In 409 Athens loses Pylos and Nisaia. Darius sends his son Cyrus to Sardis to deal with the activities on his western frontier of Persia, to eliminate the rivalry between Tissaphernes and Pharnabazus and ensure Sparta wins the war. Lysander, the new and dynamic Spartan navarch, negotiates with Cyrus. Alcibiades is back in Athens in 407 and granted full powers for the conduct of the war. Early in 406 at the battle of Notion an Athenian fleet keeping guard on Ephesus is defeated by Lysander, captured 15 ships. Alcibiades is discredited, even though he was not present and he withdraws to an estate in the Hellespont and new generals are elected. Conon is given command of the navy. Within a few months of this battle, Peloponnesians have a fleet of 140 ships, under admiral Callicratidas. Conon gets forced into battle near Mytilene and loses 30 of his 70 ships, the rest are blockaded. The Athenians melt down dedications to finance the building of more ships, promise freedom to slaves and citizenship to aliens in return for signing on as rowers. They swiftly get together fleet of 150 ships to relieve Conon at Mytilene. Callicratides leaves 50 ships to maintain the blockade, and takes 120 ships out to meet the Athenian relief fleet. A battle is fought near islets of Arginoussai, south of Lesbos, where the Athenians score a great victory; restoring Athenian domination of the eastern Aegean. Once again the Spartan offer peace, but it is rejected under the influence of Cleophon.
In 406 after the Athenian victory at the Arginoussai Islands, Conon took the fleet to the small river mouth at Aegospotami in the Hellespont. The Spartan fleet was close by on the opposite side of the Hellespont, and for four days Conon rowed his fleet over to it, trying to engage the Spartans, who for their part stayed put. On the fifth day, after repeating this manoeuvre once more, the Athenians returned, beached their ships and scattered to look for food, Aegospotami being too small to have a market. However, the Spartan commander Lysander had sent two ships as scouts, to shadow the Athenians and report back. Upon hearing that the ships were unguarded, Lysander quickly brought his troops across and burned nearly all of Conon's 170 ships, only 9 escaping in time, , the flagship Paralus returning to Athens and the others fleeing to Cyprus. 3000 prisoners are massacred. Conon wisely did not go home.
Lysander, planning to blockade Athens, expels the Athenian cleruchs from the islands to swell the population at Athens. After subjugating the Athenian cities in the Hellespont and Thrace he sailed with 150 ships into the Saronic gulf, occupied Aegina, and blockaded Pireaus. A Harmost and a group of 10 oligarchs, Lysanders friends, were installed in many of the cities. Pausanias and Agis entered Attica, encamped at the Academe, west of the city walls which were too strong to attack, the army withdrew with the onset of winter, though the fleet remained. The Athenians now made peace offers. They would give up their empire, and become an ally of Sparta. Sparta seeing blood wanted harsher terms. Theramenes visits Lysander to find out what would be acceptable and returns after 3 months to find Athens is ready to submit on any terms. Theramenes is sent to Sparta with full powers to negotiate a settlement. Sparta's Peloponnesian allies particularly the Corinthians and Boeotians wanted to destroy Athens and sell the population into slavery but Sparta remembering Athens' past service to Greece offers harsh, but reasonable terms:
If one were more cynically inclined one might think the desire to save Athens was to make her a loyal ally of Spartan policy in central Greece as a counterweight to Boeotian expansionism and step into her shoes in her former empire. Perhaps we see Lysander's hand at work here.
In April 404 after the terms were ratified, Lysander sailed into Piraeus, and began work of demolishing the walls.: Athenians and Peloponnesians worked together, to the music of flute-girls, celebrating the freedom of the Greeks.