At the time of Alexander, the Persian Empire was an unstable empire whose pieces were falling into the hands of satraps, or local lords. One of these satraps, Bagaos, killed several kings of Persia before one of his "puppets," Darius III managed to kill him. Hence the Persians were far from united against Alexander, although they managed to field impressively large armies.
Darius II was not a particularly capable commander, who was unable to lead his admittedly inferior, but much more numerous troops against those of the highly talented Alexander, at the battles of Issus and Arbela. Nor was he able to attack Alexander during his seven month siege of Tyre, between the two battles.
Darius fled each time, and after Arbela was assassinated by his cousin Bessus, who proclaimed himself King, but was captured and executed by Alexander as a rebel.