The proximate cause of the Ionian Revolt allegedly lay in the intrigues of two tyrants of Miletus. King Darius had summoned Miletus’ tyrant, Histiaeus, to his court at Susa under ostensibly honorable circumstances (Hdt. V 24) and then appointed as the new tyrant of Miletus Histiaeus’ cousin and son-in-law Aristagoras (Hdt. V 30; presumably Histiaeus had no direct male heir and in this case was succeeded by a more distant relative whom, clearly, he had groomed for the part). However, Histiaeus desired to leave Susa, and, according to Herodotus, encouraged his successor to rebel in the hope that Darius would then send him, Histiaeus, back home to deal with the revolt (Hdt. V 35). The truth of this is difficult to judge. Aristagoras, for his part, feared reprisals from Artaphernes, the Persian satrap in Sardis, after a failed attempt to conquer the island of Naxos for the Persians (Hdt. V 30-35). So for his own reasons he too planned to revolt.
The revolt’s ultimate cause emerges most clearly from the course which it took. Aristagoras voluntarily laid down his office as tyrant and helped establish a democracy in Miletus. (How “democratic” this democracy was is an open
Question - see chap. 8 and Box 13.1.) Aristagoras then engaged in a campaign against - not any Persian official, but instead the other tyrants in the various Greek cities, all of whom lost their positions in what can hardly have been other than a large-scale popular uprising. Herodotus explains that most of the tyrants escaped with the loss of their positions only, but that the people of Mytilene stoned their tyrant, Coes, to death (Hdt. V 37-38). In other words the revolt was directed in the first instance against the tyrants, not against the Persian Empire. All the same, the tyrants had ruled as exponents of the Persian Empire which had guaranteed their rule; and once the tyrants had been expelled, the rebellious Greeks had to contend with the inevitable reaction from the Empire.
Even before the Revolt - conventionally called the Ionian Revolt even if it involved all the Greeks in Asia Minor, not just those in Ionia, and additionally extended to Cyprus where various non-Greek towns joined as well - Aristagoras had traveled to mainland Greece to gain supporters. At Sparta King Cleomenes had shown him the door (Hdt. V 49-51 - see also Box 9.2), but at Athens he met with a favorable reception (Hdt. V 97).
Athens, after all, had every reason to desire to undo the Persian position in Asia Minor. Hippias still ruled in Sigeium; and the Persian satrap in Sardis had all too recently ordered the Athenians to accept Hippias as their tyrant. The Persians had been steadily extending their empire into the Aegean - the attempt to conquer Naxos just before the revolt broke out was one of many such steps - and coming ever closer to Athens. So when Aristagoras asked Athens for help in a revolt against the Persians in Asia Minor, he received it. In addition to Athens, one traditional ally of Miletus, the Euboean town of Eretria, sent aid in 499 BC (Hdt. V 99).
It was, then, with troops from Athens (and Eretria) that the rebellious Greeks of Asia Minor marched upon the Persian satrapal capital of Sardis. The revolt had evidently caught the satrap unprepared. The Greeks captured Sardis, except for the strongly defended citadel. Fire broke out and devastated the city. Shortly thereafter, additional contingents arrived to support the satrap, and the Greeks retreated towards the coast. There, at Ephesus, they lost to Persian forces. At this point the Athenians left the others in the lurch and returned home (Hdt. V 100-103).
Meanwhile, the revolt continued to grow. On Cyprus both Greeks and Phoenicians rebelled (only the Eteocyprian town of Amathus remained loyal to the Persians and soon found itself besieged by the rebels); Greek forces overran Persian holdings in the Hellespont and even took the important site of Byzantium; various cities in Caria joined the revolt (Hdt. V 103-104). All the same the Persians methodically set about putting the revolt down.