What led to conflict between the Greek city-states and the Persian Empire?

The Greek city-states within the Persian Empire in Asia Minor were restive, and two of their mother-cities in Mainland Greece, Eretria and Athens, provided military support to them. During this in 498 BCE, forces from the two cities over-reached by burning down Sardis, the Persian provincial capital of Asia Minor.

Persia mounted an amphibious punitive expedition against the two cities, capturing Eretria, but repulsed by Athens at Marathon in 490 BCE.

Persia realised that these interventions would continue, and decided to incorporate the mainland Greek cities within its empire to keep them quiet. The invasion was defeated in a series of battles at Salamis, Plataia and Mykale 480-479 BCE, and sporadic warfare ensued for the following 30 years until Persia gave up and agreed to a peace in 449 BCE under which both sides undertook to stay out of each other's territories.