In 493 Themistocles became archon eponymos in Athens. He made a start with the fortification of the three natural harbours of the Piraeus. This was a first step towards the later Athenian supremacy on the seas. A year later a number of Greek colonists from the Thracian coasts returned to Athens. Among them was Miltiades II, a nephew of the founder of the colony in Thracy. The reason was that the Persian empire had started an expedition against the coastal area of Thracy which was infected by the Ionic revolt of 499. Darius managed to prevent another revolt from happening here, but it is not known if his second goal would have been Hellas itself. Before he reached the Greek borders his fleet got damaged in an enormous storm at Athos. His army which travelled over the land had now lost its supplies and on top of that was it attacked by a Thracian tribe of nomads, so Darius wisely decided to retreat.

Return of the Persian army.

Darius was convinced that the bad co-operation between his fleet and army had been the main reason for his first failure, so for his next expedition he used a smaller fleet. In 490 the fleet crossed the Aegean and conquered several small Greek islands. In Athenian tradition this expedition is seen as a revenge against Athens and Eretria, as Darius was angry that both cities had openly attempted to interfere in the Persian empire during the Ionic revolt.

From the Persian point of view it seems more likely that this new expedition was a sequel to the one of 492 in an attempt to gain an effective control over the Aegean by strongholds in Thracy, on several Greek islands and in Athens itself. This theory becomes even more likely as the tyrant Hippias, who was banished out of Athens in 510, travelled along with the Persian fleet. The Athenians feared that the Persians hoped to make Athens indirectly a part of their empire by installing a pro-Persia tyranny.

The battle of Marathon.

In Athens Miltiades had become an important person because of his noble family and his experiences with the Persians. Besides victim of the Persians he also was a personal enemy of Hippias. In 490 he was chosen as a strategos and he managed to persuade the majority of the Athenian citizens in spite of their hesitations to fight an open battle with the Persian army. Sparta promised to help Athens. However, before the armies were gathered was Eretria, the weakest of the two guilty cities, already destroyed.

After this the Persian army landed at the northwest coast of Attica, in the plains of Marathon. Their number is not known, but it was vastly larger than the 10.000 hoplites that Athens and one small ally, Plataea, could put into the field against them. Still the superiority of the phalanx proved to be more important than the superior Persian manpower. The Spartan army was late because of religious reasons and arrived just in time to congratulate the Athenians with their miraculous victory.