However, after these victories, Mardonius’ fleet was destroyed in a storm off the coast near Mount Athos. According to Herodotus, the Persians lost 300 ships and 20,000 men. Around this time, Mardonius was commanding the army in a battle in Thrace. While Mardonius was wounded in the battle, he was victorious. Nevertheless, the loss of the fleet meant that he had to retreat back into Asia Minor. He was relieved of his command by Darius, who appointed Datis and Artaphernes to lead the invasion of Greece in 490 BC, and though they were subsequently successful in capturing Naxos and destroying Eretria, they were later defeated at the Battle of Marathon.
Mardonius came back into favour under Darius' successor Xerxes I, Mardonius' cousin and brother-in-law.. Xerxes was at first not interested in renewing the war with Greece, but Mardonius repeatedly tried to convince him that he must avenge Darius' defeat. This view was opposed by another of Xerxes’ advisors, Artabanus, who urged more caution in the matter. Herodotus, who portrays Mardonius as a somewhat evil adviser (as opposed to a number of other good advisers whose arguments are never followed), says that Mardonius simply wanted to become satrap (governor) of Greece.
He was present at the Battle of Thermopylae, and after the Persian defeat at the Battle of Salamis, he attempted to convince Xerxes to stay and fight yet another battle. This time Mardonius could not persuade Xerxes, but when Xerxes left he did become governor of those parts of Greece that had been conquered by the Persians. He subdued Macedon, ruled at that time by King Alexander I, but Alexander himself gave valuable information about Mardonius' plans to the Athenians, saying that, as a Greek, he could not bear to see Greece enslaved. Then Mardonius sacked Athens, which had been deserted before the Battle of Salamis. He offered to return Athens and help rebuild the city if the Athenians would accept a truce, but the Athenians rejected the truce and prepared for another battle.
Mardonius prepared to meet them at Plataea, despite the opposition from another Persian commander, Artabazus, who, like Artabanus, did not think that a much larger Persian army could automatically defeat the Greeks. Mardonius was killed in the ensuing battle (see Battle of Plataea).