At Miletus, an Ionian city, their hopes were to be disappointed: the city was set on a jutting headland, and as soon as its garrison commander heard that help from the Persian navy was on its way, he had changed his mind about surrender. This was disturbing news as naval support could keep this powerful position open indefinitely; as so often before, Alexander's solution lay in his speed. He captured the outer city, installed his allied Greek fleet in the harbours to block anchorage by the Persians, and set-ded down to wall off the rest of the city and besiege it into submission by slow but traditional means. Three days later, the Persians' fleet appeared in force from Egypt 400 ships strong in the opinion of Alexander's officers. For the first time in Asia Alexander was outnumbered. As he now held the strong defensive position, he need only have continued to block the city's harbour from attack and go about his siege as usual; however, the sight of Persian ships, it is said, moved Parmenion once more to offer his advice; after their dialogue at the Granicus, suspicion stirs uneasily.

Parmenion advised Alexander to attack both because he expected that the Greek fleet would win and because he was convinced by an omen from heaven: an eagle had been sitting on the shore by the stern of Alexander's ships. If they won, it would be a great help for the war as a whole: if they lost, it would not be a grave disaster as the Persians were already masters of the sea. He would go on board in person and take his share of the danger.

Alexander, however, considered that

Parmenion's judgement was wrong and his interpretation of the omen was improbable. It made no sense to fight with a few ships against many more, especially as the Cypriots and Phoenicians on the enemy side were a practised unit, whereas his own fleet was not fully trained: in an insecure position, he did not wish to surrender the experience and daring of his Macedonians to the barbarians. Defeat at sea would be a serious blow to the initial glory of the war, the more so as the Greeks would revolt if encouraged by news of a naval disaster.

As for the omen, 'the eagle was indeed in his favour, but because it had been seen sitting on dry land, in his opinion it meant that by land, he would overcome the Persian fleet'.

This refusal to fight at sea was tactically sound. It would have been foolhardy to risk a naval battle against so many ships, some of which were technically superior to Alexander's Greek fleet. They were an expert force, even if their crews were drawn from Cyprus and Phoenicia, areas where Greek culture had made its mark and revolt against Persia had been recent. It is most unlikely that the experienced Parmenion ever proposed such an indiscretion except in the pages of court history, where first Callisthenes, then Alexander's friend Ptolemy could work up his 'proposal' as a foil to their myth of Alexander. Events soon explain why they invented such a discussion; as for the eagle, bird of Zeus, it was a suitable omen for a king whom Zeus protected and it was also the symbol on the first gold coins which Alexander issued in Asia.

At first, Miletus tried to beg neutrality, but Alexander rightly refused it, and battered his way into the streets with the help of his siege engines. Many Milesian citizens 'fell in front of Alexander and implored him as suppliants, delivering themselves and their city into his hands'; these no doubt, were ordinary men who yearned for a return to democracy. But a few Milesians fought bitterly beside the hired Greek garrison until they were forced to launch into the sea and swim or paddle their way to an offshore island for safety; these, no doubt, were the richer citizens who had domineered the city with Persian support. Even on their island, they prepared to resist heroically, until Alexander intervened and offered to spare them, 'being seized with pity for the men because they seemed to him to be noble and true'. He enrolled all 300 of them in his army, no longer branding them as traitors; unlike the hordes he had punished at the Granicus, he had made them a promise in return for their surrender, and so lived up to it, not least because a mere 300 soldiers would not be a strain on his army treasury.

Mercenaries apart, a signal victory was being won out to sea. Like all warships in the ancient world, the Persians' men-of-war were like 'glorified racing-eights' and had so little room on board in which to store provisions that they were forced to remain in daily touch with a land base. Meals could not be cooked on the move and fresh water had to be collected by putting into a nearby river-mouth. Sharp as ever, Alexander had anticipated them and sent several units by land to beat them off. Thwarted and thirsty, the Persian crews sailed away to the island of Samos where they stocked with stores, perhaps with the help of its resident Athenians. On their return to Miletus, they still fared no better for water, and so gave up the struggle in the interests of their stomachs, and sailed away southwards. Having won his victory from dry land, as prophesied, Alexander took the decision which was to determine his route for the next two years; except for twenty Athenian ships who could carry his siege equipment along the coast and serve as hostages for their fellow citizens' obedience, he disbanded his entire fleet.

Even in antiquity, the merits of this bold order were vigorously disputed and at an early date, historians who had served with Alexander felt bound to defend their king's sound sense. Hence, at the beginning of the siege, they inserted a naval dialogue with Parmenion as a preface to the fleet's dismissal. Just as on the banks of the Granicus, Parmenion had been introduced into the story in order to stress Alexander's daring and play down the cautious truth, so at Miletus he was used in reverse, stressing Alexander's safe logic and smoothing over the very real risk which he was soon to take by disbanding his allied navy.

'He considered', wrote his officers, 'that as he now held Asia with his infantry, he no longer needed a fleet.' This does so little justice to Alexander's foresight that it can only be pious publicity; so far from not needing a fleet, let alone a Greek fleet, seven months later Alexander was forced to order his allied ships to reassemble in the face of the Persian counterattack which he must always have feared. His allied Greek fleet employed at least 32,000 men at the gigantic cost of some 160 talents a month and despite the treasures of Sardis and the hopes of tribute and contributions, he was seriously worried about his finances; his Greek allies were presumably not obliged to pay for their crews' upkeep, an imposition which was only tried later in a special case. The following spring, he could send 600 talents home to Antipater and a further 500 to finance the recruitment of his second allied navy, but this surplus may not have been ready at Miletus and anyway, tactics, as much as money, were at the root of the dismissal. Outnumbered, and unable to risk a head-on engagement against superior crews, 'Alexander thought that by capturing the coastal cities he would break up the Persian fleet, leaving them nowhere to recruit crews or use as a seaport in Asia'. In view of an ancient warship's dependence on its land base for daily supplies, Alexander had calculated this strategy shrewdly. On a lesser scale, it had worked already at Miletus and reapplied, it would eventually force the Cypriot and Phoenician ships to surrender and join his side. Friends later passed off the strategy as safe and free of risk, but it needed two years' faith and patience to succeed. During this time the Persian fleet threatened the entire Aegean, regained the use of many harbours which Alexander thought he had closed, and might, with more luck, have forced him to return to the Asian coast. It was a strategy shot through with short-term danger. Nevertheless finance and numbers made it the one sound option. Alexander, at least, had the foresight and daring to pursue it to its hazardous end.