The siege of Miletus (494 BC) followed the Ionian naval defeat in the battle of Lade, and saw the Persians recapture the city that had triggered the Ionian Revolt in 499.
The revolt had originally been led by Aristagoras, tyrant of Miletus. He had fled from the city during the first major Persian counterattack in 497-496 and died in a minor siege in Thrace, but the Persians still considered Miletus to be their most important enemy.
In 494 the Persians raised a 600-strong fleet and a large army, and advanced towards Miletus. The Ionians managed to gather a fleet of 353 ships, which they posted at Lade, then an island just to the west of Miletus (since then the Maeander River has silted up its estuary and both Miletus and Lade are now inland.
When the Persians attacked the Ionian fleet fell apart, with several contingents deserting the cause (starting with the Samians, and then the Lesbians). The part of the fleet that did stay and fight suffered a heavy defeat, and the survivors scattered back to their home cities (or even further afield in some cases).
This left Miletus isolated in the face of the Persian army. The Ionians had decided to focus most of their effort on the fleet, leaving the Milesians to defend their own city.
The resulting siege appears to have been quite lengthy. Herodotus records that the Persians undermined the walls, and other sources suggest that battering rams were used as well. Eventually the city was captured, and devastated. According to Herodotus the Persians killed most of the men, enslaved the women and children and destroyed the shrines at Didyma. Archaeological evidence supports the idea that there was significant destruction at this point, and the harbour area was abandoned. Miletus had been one of the great cities of the Greek world, but it took centuries for it to recover from this blow.
The Persians then went on to restore control of the rest of Ionian and the remaining rebel cities in the Hellespont area. In 494 and the first part of 493 they acted with a similar level of ferocity as at Miletus, but eventually they adopted a more conciliatory approach, which helped restore some normality to the area.