The Governor then resolved to set out at once for the Red Sea. King Emmanuel, whose main idea it was to close this route to commerce, had directed him to dismantle the fortress on the island of Socotra, owing to the difficulty of getting provisions, and to occupy Aden instead. When this decision became known, Diogo Mendes, who had been specially ordered to Malacca, murmured loudly, and declared his intention of leaving the Governor and at once departing with his squadron westwards. Albuquerque expostulated with him; he pointed out that four ships could not conquer the Malays, and argued that their treatment of the first Portuguese squadron showed that they would not permit the Portuguese to open up trade without first being defeated. He even showed Diogo Mendes a letter which had arrived from the Portuguese Factor left at Malacca, stating that he and his comrades were kept as prisoners. He promised that, as soon as the King's commands with regard to the Red Sea had been carried out, he would himself proceed with a powerful fleet to the Malay Peninsula, and firmly establish Portuguese influence in that quarter.
Diogo Mendes felt the force of these arguments, but the master of his flagship, Dinis Cerniche, would not agree, and setting sail crossed the bar of Goa harbour on his way out. The Governor at once sent a ship, under Jaymé Teixeira, with orders to make Mendes return by any means in his power. Since the master would not shorten sail, the ship was fired on and forced to return by the destruction of its main yard. Albuquerque forgave Mendes, but ordered Cerniche to be executed, which sentence was not carried out, but the master was instead sent back to Portugal in custody. Nevertheless the persistency of Mendes and his men seems to have greatly influenced Albuquerque, for finding in Feb. 1511, when he sailed out of Goa harbour, that it was impossible to sail westward owing to the monsoon, he resolved to make his way to Malacca. He first sailed to Cochin, where he appointed Manoel de Lacerda to be Captain of the Indian Sea with supreme authority, and he directed that Lacerda's orders should be obeyed as if they were his own.
Albuquerque's conquest of Malacca ranks second in importance among his great feats of arms to the capture of Goa. It gave the Portuguese the complete command of the spice trade, and eventually of the Chinese and Japanese trade. It struck the final blow at the Muhammadan commercial routes to Europe. Hitherto the Portuguese had only secured the monopoly of the Indian trade, and Muhammadan vessels, largely manned by Arabs, still collected the produce of Bengal and Burma, of Sumatra and the Spice Islands, of Siam and China, at the great commercial port of the Malay Peninsula. Albuquerque resolved to check this trade by holding the mouth of the Red Sea, but it seemed to him of even more efficacy to seize upon the headquarters of the trade itself.
The city of Malacca, with its splendid harbour, was the capital of a wealthy Muhammadan Sultan. This man's ancestors were said to have come from the neighbouring island of Java, and to have been converted to Islám some 200 years before. Constant war had been waged between the Kings of Siam, who formerly ruled the whole peninsula, and the Javanese immigrants; but the latter had held their own, and by a wise encouragement of commerce had become very wealthy and powerful. The trade of Malacca with India is said by the Portuguese chroniclers to have been largely in the hands of merchants from Gujarát, and when the Portuguese conquered the city it was inhabited by men of nearly every Eastern race, Hindus from both sides of India, Arabs, Chinese and Javanese. It is mentioned that on their arrival they found, among other officers, four men holding the title of Xabandar (Sháh-i-Bandar) or Captain of the Port. These four men are expressly stated to have been governors of different districts, and they are said to have belonged to four different nationalities and to rule over the Chinese, the Javanese, the Gujarátís and the Bengalís respectively. This division probably fairly indicates the chief nationalities of the merchants of Malacca.
Malacca was first visited by a European squadron on September 11, 1509. Diogo Lopes de Sequeira had been despatched by King Emmanuel with instructions to explore the island of Madagascar, and afterwards to proceed to the Malay Peninsula, which was well known to the Portuguese king by its classical name of the Golden Chersonese. The arrival of Sequeira in India during the viceroyalty of Almeida has been already noticed, and mention has been made of the Viceroy's wish that he should take over the government in the place of Albuquerque. Sequeira declined this offer and sailed for the Malay Peninsula with his squadron of five ships, but he so far complied with the Viceroy's wishes as to carry with him the chief friends of Albuquerque, and notably his most constant supporter, Ruy de Araujo.
Sequeira visited Sumatra, and safely reached Malacca. He was favourably received at first by the Sultan, and sent ashore Ruy de Araujo to fill the perilous post of Factor. As a lucrative trade seemed likely to spring up, the Portuguese captain proceeded to land a large quantity of goods together with several Portuguese clerks. But as usual the Muhammadan merchants soon showed their jealousy of the Portuguese, as they had always done on the Malabar coast. The Bendara, or native Prime Minister of Malacca, listened to the suggestions of the Moslem merchants, and formed a plan to destroy the whole Portuguese squadron. It was resolved to invite all the officers to a grand banquet at which they should be suddenly murdered, and in their absence it was believed that the ships might be easily taken. A Javanese woman, who had fallen in love with one of the Portuguese, swam out to their ships and gave warning of the plot. The Portuguese officers in consequence declined to land, and as soon as their determination was made known, the Malays set upon the factory, and made Ruy de Araujo and about twenty men whom he had with him prisoners.
They defended themselves gallantly, but Sequeira made no effort to assist them, and sailed away out of the harbour. He was obliged before leaving the peninsula to burn two of his ships for want of men to navigate them, and with the other three he made his way to India. When he reached the Malabar coast and touched at Caecoulão (Káyenkolam), he heard that the Marshal had placed Albuquerque in power, and that Almeida had departed. Sequeira, fearing the vengeance of Albuquerque, at once set sail for Portugal, sending his other two vessels under the command of Nuno Vaz de Castello-Branco to join the Governor at Cochin. It was to wreak vengeance on the Sultan of Malacca and to open up trade there that the squadron of Diogo Mendes de Vasconcellos had been sent from Portugal in 1510; but, as has been related, in spite of the captain's wishes, he and his men had been detained by Albuquerque to take part in the second capture of Goa.
Ruy de Araujo wrote a pathetic letter to Albuquerque, describing the manner in which he and his companions were treated. He told his friend that there were nineteen Portuguese alive at Malacca, who had been greatly tortured to make them turn Muhammadans. He also said that they had been very kindly treated by a Hindu merchant, named Ninachatu, who had secured the means for the despatch of the letter. He begged Albuquerque, for the love of God, to keep them in remembrance, and rescue them out of their captivity; and he also requested that the kindness of the Hindu merchant should not be made known for fear that the Moslems of the Malabar coast should give information to their co-religionists at Malacca.
It may well be imagined that Albuquerque was not sorry to go to the rescue of the Portuguese prisoners. He would have postponed this duty in order to obey the king's express commands; but now that the winds forbade him to sail East, he determined to sail West. He started with eighteen ships, carrying 1400 men; and though he lost one galley at sea, he arrived safely at the port of Pedir in the island of Sumatra in May 1511 with the rest of his fleet. At that place he found nine of the Portuguese prisoners, who had escaped from Malacca, and he then made his way slowly to the great city, which was said to contain a population of over 100,000 inhabitants.
For weeks negotiations went on with the Sultan of Malacca. The main point at issue was the surrender of Ruy de Araujo and his fellow-prisoners. Albuquerque declared he would make no treaty with the Sultan until the prisoners were delivered, and the Sultan on his part was resolved not to give them up until a treaty of peace had been signed. Under these circumstances Albuquerque wrote to the Factor, telling him that he and his companions must bear their hardships with patience. Ruy de Araujo replied in terms which show the gallant spirit of the Portuguese at that period.