In 499 BC, Artaphernes received an embassy from Athens, probably sent by Cleisthenes. Artaphernes advised the Athenians that they should receive back the Athenian tyrant Hippias. The Persians threatened to attack Athens if they did not accept Hippias. Nevertheless the Athenians preferred to remain democratic despite the danger from Persia. Soon after this, the Ionian Revolt began.
Subsequently Artaphernes played an important role in suppressing the Ionian Revolt.
Athens and Eretria responded to the Ionian Greeks’ plea for help against Persia and sent troops. Athenian and Eretrian ships transported the Athenian troops to the Ionian city of Ephesus. There they were joined by a force of Ionians and they marched upon Sardis.
Artaphernes, who had sent most of his troops to besiege Miletus, was taken by surprise. However, Artaphernes was able to retreat to the citadel and hold it. Although the Greeks were unable to take the citadel, they pillaged the town and set fires that burnt Sardis to the ground. Returning to the coast, the Greek forces were met by the Persians, led by Artaphernes, who overpowered the Greeks.
Having successfully captured several of the revolting Greek city-states, the Persians under Artaphernes laid siege to Miletus. The decisive Battle of Lade was fought in 494 BC close to the island of Lade, near Miletus' port. Although out-numbered, the Greek fleet appeared to be winning the battle until the ships from Samos and Lesbos retreated. The sudden defection turned the tide of battle, and the remaining Greek fleet was completely destroyed. Miletus surrendered shortly thereafter and the Ionian Revolt effectively came to an end.
After the revolt was put down, Artaphernes forced the Ionian cities to agree to arrangements under which all property differences were to be settled through references to him. Artaphernes reorganized the land register by measured out their territories in parasangs and assessed their tributes accordingly (Herodotus vi. 42). The Milesian historian and geographer Hecataeus advised him to be lenient so as not to create feelings of resentment amongst the Ionians. It seems that Artaphernes took this advice and was reasonable and merciful to those who had recently revolted against the Persians.
His son of the same name was appointed, together with Datis, to take command of the expedition sent by Darius to punish Athens and Eretria for their roles in the Ionian revolt. Ten years later, he was in command of the Lydians and Mysians (Herod. vi. 94, 119; Vu. 4, sch. Persae, 21).
Aeschylus, in his list of Persian kings (Persae, 775 ff.), which is quite unhistorical, mentions two kings with the name Artarenes. Aeschylus may actually be referring to both Artaphernes and his son of the same name.
Artaphernes derives from the Median: Rta + Farnah (endowed with the Glory of Righteousness). The equivalent to Rta in Middle Persian is Arda-/Ard-/Ord- as seen in names such as Ardabil (Arta vila or Arta city), Ardavan (protected or protecting Arta) and Ordibehesht (the best Arta). Arta is a common prefix for Achaemenid names and means correctness, righteousness and ultimate (divine) truth. Farnah is the Median cognate of Avestan Xvarənah meaning "splendour, glory". Farnah is an important concept to pre-Islamic Persians as it signifies a mystic, divine force that is carried by some important or great individuals. So Artafarnah can be said to mean "splendid truth". The concept of "arta" is also mirrored in the Vedic civilization through the Sanskrit word "ŗtá", or righteousness.
From Cyrus to Alexander: A History of the Persian Empire (2002).