The battle of Issus (333 B.C.) witnessed the destruction of Darius III's western army. Alexander now, realistically, was faced with two choices. Should he pursue Darius into Mesopotamia, or continue his policy of conquering the Asiatic coast to deny the Persians access to the sea? Obviously he chose the later, but here we shall try to understand why.
As he fled East, Darius doubtless expected to look back at any moment to find Alexander pursuing him. But Alexander had decided that following Darius into the depths of Asia was, for the moment, not a good idea. He cannot have known in the aftermath of Issus where Darius was going or what he planned. What he will have known is that the Persian Empire still possessed great reserves of manpower in the East. And this was a real threat to Alexander, particularly as the situation in the West was still in flux. The last thing Alexander needed was to move inland while potentially dangerous forces remained to his rear, particularly as Darius might retreat to the mountains and wage a guerilla campaign which might take years to subdue.
The Persians had suffered a shattering defeat, but they still possessed significant forces in the west. Of chief importance, and the greatest threat to Alexander's fledgling empire, was the fleet which was operating in the Aegean. The commanders Pharnabazus and Autophradates had been charged with provoking and supporting rebellion on the Greek mainland, under the leadership of Sparta, and reconquering the Aegean islands and Anatolian coast. Prior to Issus they had made progress, capturing a number of the Greek islands and forcing Alexander to rebuild his navy.
When the news of Issus reached the Persian Admirals they sailed to the coast of Asia Minor to head off the inevitable revolts which news of the battle would provoke. By Spring 332 the fleet had essentially collapsed, the Phoenician and Cypriot ships leaving for home. If Alexander had not moved south along the coast would these troops have abandoned the Persian cause? The fleet had caused Alexander a great deal of trouble, but no longer. After the capture of Tyre, the Macedonians, with their new Phoenician and Cypriot allies were the masters of the Eastern Mediterranean.
A large body of troops had fled from Issus to the north and linked up with Persian forces in Anatolia. These represented a real threat to Macedonian control of the region, which at this point was by no means assured. Alexander kept faith in Antigonus to deal with the situation. He did so, but it took three pitched battles and over a year of fighting to defeat these Persian loyalists. While our sources, obsessed as they are with Alexander, have paid scant attention to these events, the situation in Anatolia seems to have been fairly serious. Alexander, not blessed with hindsight, would have been well aware that this region must be pacified in order to assure the success of his future campaigns. The news that Antigonus had finally crushed the resistance must have been welcome indeed.
Another group of mercenaries fled from Issus to Cyprus. From here, Amyntas, a Macedonian fugitive, led some of them to Egypt with the aim of annexing the country. This was a canny bit of opportunism on Amyntas part. As Ptolemy was to prove later, Egypt, when properly defended, was a daunting natural fortress. If Amyntas had been successful, it would have proven hard to dislodge him. Some historians have questioned the wisdom of Alexander pushing into Egypt, after subduing Phoenicia. What they seem to have misunderstood is that, if Alexander had not taken the province when he did, if he had let Amyntas, or some other commander, dig himself in and use the provinces wealth to hire a mercenary army, he might never have captured it. Indeed, as Ptolemy again proves, a capable ruler in Egypt was well placed to attack Phoenicia and dominate the Eastern Mediterranean. Fortunately for Alexander, Amyntas was defeated and killed by the Persian troops stationed in Egypt. Amyntas' defeat seems to have rested more on the indiscipline of his troops rather than the skill of the Persian garrison who, later, surrendered to Alexander. But a year or two down the line, and with effective leadership, the situation may have been very different. Moreover, Alexander was already thinking in terms of establishing himself as master of Asia. For this reason also he was unwilling to leave Egypt's future in the hands of fate.
While it may seem that Alexander had a choice of strategy after Issus, I would contest that this was illusionary and that circumstance dictated precisely which course he had to follow. The need to deal with the various Persian forces still active in the West and to bring the coastal provinces securely under his control, in order to advance his claim to legitimate kingship, out weighed by far any desire to pursue Darius.