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 The men had consequently suffered severely, and, contrary to the company's orders, the fleet was obliged to stop for a month at the Cape. On 19 Dec. they made the coast of Sumatra, and anchored at Bantam on the 23rd, the men being, by this time, again at the last extremity of weakness. On 18 Jan. 1604–5, Middleton, in the Dragon, with the Ascension, went on eastwards, and the Hector and Susan were ordered home with cargoes of pepper. The men were at this time dying fast; twenty-six are named as having died on board the Dragon between leaving Bantam and anchoring at Amboyna on 10 Feb. And just at this time the Dutch seized the island, and so put an end to all chance of trade there. After long debate and with much misgiving, the Ascension and Dragon resolved to separate, the former going to Banda, the latter to the Moluccas. They sailed from Amboyna on 18 Feb., and on 22 March after a tedious voyage the Dragon got off Tidore, where the Portuguese had a settlement, and were supporting the natives in a war with their neighbours at Ternate, who were aided by the Dutch. Middleton's force was too insignificant to permit of his taking any part in the quarrel, which ended in the complete defeat of the Portuguese. The Dutch then threw every possible obstacle in the way of the English trade; and though Middleton managed, here and there, to pick up some cloves, it does not appear that he had anything like a full cargo when, on 24 July, the Dragon anchored again at Bantam. She sailed for England on 6 Oct., and on 19 Dec., standing in for Table Bay, sighted the Hector in the last extremity of distress, almost all her men being dead. Middleton sent men on board to take her into the bay, where they stayed for a month, and where they were joined by the Ascension. They sailed on 16 Jan., and, after touching at St. Helena, anchored in the Downs on 6 May 1606. Middleton's services were promptly recognised. He had pushed his voyage much further than the company had dared to order him, and the profits were very great. He was knighted at Greenwich on 25 May 1606; and ten years later he was still described as ‘the thrice worthy general who laid the true foundation of our long desired Cambaya trade’ (, The Defence of Trade, p. 23).

In 1610 Middleton was appointed to command the sixth voyage set forth by the East India company, and sailed from the Downs on 4 April in the Trade's Increase, having in company the Peppercorn, commanded by Nicholas Downton [q. v.], and the Darling. The voyage out was comparatively fortunate, and there was no exceptional sickness when, on 7 Nov., they arrived at Aden. Leaving the Peppercorn there, Middleton, with the Darling, went on to Mocha; but in entering the roadstead, in charge of a native pilot, the Trade's Increase was run ashore, and much of her cargo and stores had to be landed before she could be floated off. The governor, or aga, received Middleton and the merchants with every appearance of friendship; but a few days later, 28 Nov. when a large working party was on shore, he suddenly attacked them, killed eight in the scuffle, and made prisoners of Middleton and the others, to the number of fifty-nine. He then attempted to seize the Darling, which was lying close in shore; but in that the Turks were repulsed with heavy loss. For more than three weeks the prisoners were kept at Mocha, heavily ironed; they were then sent to the bashaw at Sinan (Sana), where they were more humanely treated and allowed to communicate freely with the ships. Downton, who had arrived from Aden in the Peppercorn, proposed making reprisals on the Turkish and Indian trading vessels, but Middleton restrained him, fearing that ‘it might prove prejudicial to him and his company.’ The bashaw, he said, had promised that they should all be set free at the coming of the westerly winds; if he suspected any breach of faith, he would make his escape. And when he learnt that a fleet of galleys was expected from Suez, and that the aga was negotiating for the hire of some of the larger country ships which Downton had allowed to come to Mocha, Middleton, on 15 May 1611, with fifteen of his men, did make his escape, got on board the Darling, and sent orders to Downton to join him at once with the other ships.

He then, by a strict blockade of the port, compelled the Turks to send back all the men who remained in captivity, and to restore the goods which had been seized on shore, or to pay compensation for the loss, and after refitting at Socotra, he went to Surat, where he arrived on 26 Sept. He found the place closely blockaded by a Portuguese fleet of eighteen frigates, which made communication with the shore difficult, and prevented fresh victuals or refreshments being sent off for the men who were suffering from scurvy. After some skirmishing the prohibition to trade was partially withdrawn; but the governor was in too great dread of the Portuguese to receive the English with any appearance of friendship. He refused them permission to establish a factory, and after a stay of four months ordered them to leave. The merchants on shore were also ordered away, no