Despite Alexander's expectations of an ambush, Babylon readily surrendered to him. He rested his army there for over a month, indulging in the city's luxury. Before leaving, Alexander surprised many by reinstating Mazaeus as the satrap–a surprise since the general had battled against Alexander just a month before. There were practical reasons for Alexander's decision, as he wanted to win the support of Iranians in neighboring states. The decision also reflects Alexander's vision for the empire, which included cooperation and the peaceful incorporation of the Persians.

Again, the Macedonians proceeded to win over city by city, including the very prosperous Susa, usually without a fight. Alexander then set his sights on Persis, and in particular its capital Persepolis, one of the most venerated Persian cities, whose loss would be devastating to Darius. At the entrance to Persis, Alexander faced an impenetrable wall held by Ariobarzanes, the province's satrap. The wall had been constructed so that only a frontal attack was possible, yet efforts to this end proved futile.

However, Alexander once again had the good fortune to find a Persian prisoner who offered to show a path that would allow Alexander's forces to come out behind the Persian wall. The difficult twelve-mile path took almost two days, but the ambush left the surrounded Persians helpless. Despite his recent restraint, Alexander allowed the plundering of the city, and even participated in the burning of the city palaces himself. Though Alexander received condemnation for this indulgence, his behavior here did have one ironic side effect. Persepolis, which was never rebuilt, became a ghost town, and today it serves as a rich source for archaeologists and one of the few non-Greek sources for Persian history. Between Babylon, Susa, and Persepolis, Alexander had accumulated about 180,000 talents–estimated at approximately forty-four million pounds sterling by the 1913 standard. In comparison, Athens, the wealthiest Greek city-state at the time, had a total revenue of only 400 talents annually.

Alexander's hunt for Darius continued, but was halted with the shocking news broke that Darius had been deposed. Darius had always had rivals in the nobility, and the weakness revealed by Alexander's invasion had increased Darius's unpopularity considerably. The revolt against him was led by Nabarzanes and Bessus, who assumed the title of Great King. They placed Darius in chains and headed for Bactria, where Alexander now planned to meet them. Darius allegedly refused to mount a horse, and his awkward wagon slowed down the escape, so the conspirators ran him through with javelins and left him to die. When Alexander came upon the dead king, he sent the body to be buried with full honors at Persepolis, where the other Persian kings were buried. Although Alexander is said to have been moved by the site of Darius's dead body, the murder was convenient for Alexander; taking the king alive would have given the opposition reason to remain hopeful, while executing him would have alienated all of Persia. With Darius dead, Alexander became the undisputed ruler of Persia.

Alexander soon turned his attention again to domestic difficulties, one of which was the powerful influence wielded by Parmenion. Though the general himself was old, Alexander continued to resent his influence over the army, and he had reason to fear the ambitions of Parmenion's family. By a series of coincidences, Alexander was able to implicate Parmenion's son Philotas in a conspiracy, though the only real offense was that Philotas did not immediately report a conspiratorial incident he uncovered and dismissed as ludicrous. The trial of Philotas, which traditionally took place before the army, was a farce, and Philotas's solid defense was soundly rejected. Philotas was then tortured until he implicated his father. The son was stoned to death the next day, the father assassinated shortly afterward. These murders, along with the murders of several other potential rivals, though unjust, gave Alexander an even tighter grip on the kingdom.