While Alexander continued to defeat Persian forces on land, the Persian fleet attempted to provoke the League fleet to battle. Despite Parmenion's urging, Alexander had several reasons to avoid combat. First, he feared that a defeat would expose a weakness and encourage rebellion in Greece. More important, he recognized that he had little to gain from engagement, as he could more gradually dissolve the Persian fleet by cutting off its access to the ports he controlled. Alexander therefore made the momentous, if risky, decision to disband the League fleet and maintain only twenty Athenian ships.

After Miletus, Alexander's next objective was Caria, which had been ruled by Pixodarus, the satrap who tried to marry his daughter to Alexander's half-brother. Pixodarus himself had forced his sister, Ada, out of power, so Ada now sought to ally her faction with Alexander, Pixodarus having died shortly before. Before invading the city, Alexander therefore stopped in Alinda, where Ada was living in exile. She adopted him as her son, and he gained the loyalty of her significant faction. Alexander's first aim was to dismantle Halicarnassus, the capital city of Caria.

Leading the defense of Halicarnassus was Memnon, the mercenary general whom Alexander faced at Granicus. Despite the implicit insult to the Persian nobility, Darius, the Persian king, had appointed Memnon as governor of the coastal regions of Asia Minor, as well as the admiral of the fleet. The Persians had some early successes, but the Macedonians gradually wore them down. The turning point came when the Persians launched a surprise offensive, which came close to overpowering the Macedonians until the veteran soldiers of the phalanx joined the battle. Again, superior discipline won out, as the Macedonians gradually pushed the Persians back to their city. During the rush to their gates, the Persians were forced to shut out some of their own men in order to keep the Macedonians out of the city–some 1,000 fell in this manner. Though the Persian attack was valiant, Memnon's failure made the city's fall inevitable, and he was forced to sneak his fleet and the remaining mercenaries away.

The difficult siege tested the Macedonians considerably–and it cost them many men–but their success meant the securing of another major naval base. Alexander returned the state to Ada, though he would install his own ruler in Caria after her death. Winter was approaching, a time when battles traditionally ceased. Alexander even sent all newly married men home on leave, a move that greatly bolstered his popularity.

The winter would not be a complete vacation, however. Alexander still had hopes of reducing the remaining Persian bases along the coastline, so that an assault on its center could be started in the spring. One particular challenge involved the crossing of the Climax gorge along the shorter but more challenging seashore route, rendered impassable when strong southerly winds raised the water level. The winds changed direction just before the party reached the Climax, and they were able to pass with little difficulty. This fortunate turn was seen as divine intervention, as if the sea had withdrawn in deference to Alexander. Soon the first year of the campaign was nearing its end. All of the Greek cities had been liberated from Persian rule, but the Macedonians had yet to face a full-scale imperial army.

Alexander met up with Parmenion's army in Phrygia. The Macedonians continued to overcome city after city. The Persians would often clear out before Alexander arrived, but only after burning everything that would have been useful to him. Concerned about the failure of his satraps and generals to hinder Alexander's troops, Darius prepared to meet them with his own army.

Alexander made the mistake of assuming that Darius would meet him in Sochi, whereas Darius instead pursued him from behind. Darius then set up a defensive position on the Pinarus River, thus cutting off the Macedonian line of retreat and pinning them in on a narrow coastal plain. The situation looked disastrous for Alexander, for Darius's position at Issus was the dream of all generals before twentieth-century warfare.

The Macedonian forces, combining Alexander's and Parmenion's, totaled about 50,000; the Persians numbered about the same. The fighting was fierce, brimming with the hatred between the Greek mercenaries and the Macedonians. In many ways the battle was a repeat of Chaeronea, where Philip had led the victory of Thebes and Athens. The battle lasted about two hours, but it was largely decided in the first few minutes, when Alexander led a quick attack that broke down the Persian left wing. Darius fled and escaped, despite Alexander's pursuit into the night. The victory celebration was elaborate nevertheless, as the Macedonians tasted the exotic luxuries of Persia for the first time.

Again, the precarious nature of Alexander's rule revealed itself back in Greece each time Persia seemed to gain an advance. In Athens, Demosthenes got news of Darius's strategic placement and openly gloated at the apparently imminent Persian victory. In the Peloponnese, the Spartan king prepared a rebellion against the Macedonians and began communications with Persia for aid. Of course, news of Alexander's victory quickly crushed these hopes, and plans were once again put off for the meantime.

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