What started the conflict between the Persian Empire and the independent Greek city-states?

Answer 1

As the Persian empire expanded, it incorporated hundreds of Greek city-states dotted around the Black and eastern Mediterranean seas. These cities were originally coonies of cities in mainland Greece, and called on them for assistance, resulting in intervention.

Persia decided to incorporate the cities of mainland Greece into its empire to establish an ethnic frontier and avoid these troubles. Some cities were brought in by establishing puppet regimes, others resisted and Persia invaded in 480 BCE to take in the cities of central and southern Greece by force.

They eventually lost, withdrew and were involved in intermittent war until a treaty compromise in 449 BCE.

Answer 2

In 499 BCE the Greek Ionian city-states in Asia Minor revolted against Persian rule. The Greek mainland Ionian cities of Eretria and Athens sent military expeditions to help the Ionian cities, and although this failed, they had burnt down the Persian provincial capital of Sardis.

Persia sent a punitive expedition in 490 BCE to retaliate and establish tyrants to keep them quiet in future - this expedition was defeated at Marathon.

The Persians decided that the only way to keep the mainland cities from disrupting the peace of their empire was to extend control over mainland Greece, appoint a Persian provincial governor and pliable Greek rulers for each city. They brought some of the cities under control by bribery, and mounted a major invasion to deal with the southern cities which held out.

This invasion of 480-479 BCE failed and sporadic warfare went on for another 30 years until the Persians gave up trying to enforce peace, and left the Greek citiy-states to go back to their usual wars amongst each other.