Having firmly established the Portuguese power on the African coast, Dom Francisco de Almeida continued on his way to India. His fleet consisted of fourteen ships and six caravels, and carried 1500 soldiers. On reaching the Malabar coast he first punished the Rájás of Honáwar and Cannanore, and then established his seat of government at Cochin. The Viceroy next sent his son Dom Lourenço de Almeida, who had been appointed Chief Captain of the Indian Sea, to attack Quilon. The Moplas in that city, in spite of the lesson taught to them by Pacheco, had not ceased their intrigues against the Portuguese; and soon after Almeida's arrival they rose in insurrection and killed Antonio de Sá, the factor, and twelve other Portuguese subjects. Dom Lourenço, who was but eighteen years of age, and who soon made for himself a reputation for daring and valour unequalled in the East, bombarded and practically destroyed the city of Quilon. The young captain then visited the island of Ceylon, which had not yet been explored by the Europeans. The native prince on whose coasts he landed received Lourenço with great pomp, recognised the suzerainty of the King of Portugal and promised to provide the Portuguese ships with cargoes of cinnamon. From Ceylon also Dom Lourenço brought the first elephant ever sent to Portugal.
After his return to Cochin the Viceroy despatched his gallant son to meet a fresh fleet which had been prepared by the Zamorin of Calicut. On March 18, 1506, with but eleven ships of war under his command, Lourenço de Almeida attacked the Zamorin's fleet of eighty-four ships and a hundred and twenty prahs or galleys. The sea-fight which followed was chiefly an artillery combat; most of the Zamorin's ships were sunk, and it is said that 3000 Muhammadans perished and not more than six or eight Portuguese. The young captain sailed northward with his victorious fleet, but was repulsed in an attack on Dábhol, an important port belonging to the Muhammadan King of Bijápur. In the following year Dom Lourenço de Almeida continued his series of victories, and on November 23, 1507, with the assistance of Tristão da Cunha, who had just arrived in India, he sacked the port of Ponáni, then, as it still is, a religious centre of the Mopla community.
Meanwhile the danger which King Emmanuel had foreseen was coming to pass. The Mameluke Sultan of Egypt perceived that his income from the passage of the Indian trade through Cairo was seriously diminishing, and he resolved to make a great effort to expel the daring European intruders from the Eastern seas. He therefore prepared a large fleet, which was placed under the command of the Emir Husain, an admiral of high reputation, whom the Portuguese chroniclers call Mir Hocem. This was the first regular war fleet which the Portuguese had yet met. The fleets of the Zamorin, which Pacheco and Dom Lourenço de Almeida had defeated, consisted only of merchant ships roughly adapted for war by the Mopla traders of Calicut. The fleet of the Emir Husain, on the other hand, was a regular war fleet; it was largely manned by sailors who had experience in fighting with Christian fleets in the Mediterranean, and who understood the use of artillery quite as well as the Portuguese.
The Egyptian admiral in 1508 sailed from the Red Sea for the coast of Gujarát, where the Muhammadan King of Ahmadábád and the Muhammadan Nawáb of Diu, Málik Ayaz, had promised to receive and assist him. Dom Lourenço de Almeida was unable to prevent the junction of the Egyptian and the Diu fleets, and on their approach to his station in the port of Chaul he boldly sailed out and attacked them. His numbers were totally inadequate, but he had received express orders from his father to endeavour to prevent the allies from coming south to Calicut to join the Zamorin. For two days the Portuguese maintained a running fight, but Dom Lourenço de Almeida soon found that he had to deal with more experienced and warlike foes than the merchant captains he had so often defeated. His ship was surrounded on every side; his leg was broken by a cannon-ball at the commencement of the action; nevertheless he had himself placed upon a chair at the foot of the mainmast and gave his orders as coolly as ever. Shortly afterwards a second cannon-ball struck him in the breast, and the young hero, who was not yet twenty-one, expired, in the words of Camoens, without knowing what the word surrender meant. Málik Ayaz treated the Portuguese prisoners whom he took kindly. He wrote to the Viceroy regretting that he was unable to find Dom Lourenço's body to give it honourable burial, and congratulated the father on the glory the son had acquired in his last combat.
At this juncture Affonso de Albuquerque, who had been sent from Lisbon with a commission to succeed Dom Francisco de Almeida, at the close of the latter's three years tenure of office, made his claims known. The Viceroy, however, refused to surrender his office or to abandon the government until he had avenged his son's death. Albuquerque told the Viceroy that it was his privilege to fight the Egyptian fleet, but he felt for the father's feelings and allowed Francisco de Almeida to sail northwards without further pressing his rights. The Viceroy first relieved the fortress of Cannanore, which was being besieged by the Moplas and gallantly defended by Lourenço de Brito, and he then attacked Dábhol with a fleet of nineteen ships. He stormed Dábhol and wreaked a horrible vengeance, which passed into a proverb, on the inhabitants in December, 1508. On February 2, 1509, Dom Francisco de Almeida came up with the united fleet of the Muhammadans under Emir Husain and Málik Ayaz off Diu, and after a battle which lasted the whole day a great victory was won, in which the Muhammadans are said to have lost 3000 men and the Portuguese only twenty-two.
After the victory the powerful Muhammadan King of Ahmadábád or Gujarát, Mahmúd Sháh Begára, disavowed the conduct of Málik Ayaz, his tributary, and made peace with the Portuguese. He refused to surrender the Emir, but he gave up the Portuguese prisoners who had been taken in the previous engagement as well as the remains of the Egyptian fleet. On his return to Cochin, Dom Francisco de Almeida again refused to hand over the government to Albuquerque, and imprisoned his destined successor in the fortress of Cannanore.
However, on the arrival of Dom Fernão de Coutinho, Marshal of Portugal, the Viceroy was forced to abandon this attitude, and he left Cochin on November 10, 1509. On his way home he was obliged to put in to refit at Saldanha Bay, where his sailors had a dispute with some Kaffirs whose sheep they had stolen. Dom Francisco de Almeida went to their help, but he was struck down and killed with an assegai. Thus died the first Viceroy of Portuguese India on March 1, 1510, and it is a strange irony of fate that the famous conqueror of the Muhammadan fleet, who by his victory assured the power of the Portuguese in the East, should die by the hands of ignorant African savages.
The policy of the first Viceroy of India was not so grandiose as that of his successor. He did not believe in building many forts or attempting to establish direct government in the East. He argued that Portugal had not sufficient inhabitants to occupy many posts, and his view was that the Portuguese fleets should hold the sea and thus protect the factories on land. Any idea of establishing a Portuguese dominion in Asia seemed visionary to the first Portuguese Viceroy, and in this respect his policy differed entirely from that of his successor, Affonso de Albuquerque.
A letter from Francisco de Almeida to Emmanuel is published by Senhor Lopes de Mendonça in the Annaes das Sciencias e Letteras for April, 1858, and reveals the Viceroy's policy. In it he says:—
'With respect to the fortress in Quilon, the greater the number of fortresses you hold, the weaker will be your power; let all our forces be on the sea; because if we should not be powerful at sea (which may the Lord forbid) everything will at once be against us; and if the King of Cochin should desire to be disloyal, he would be at once destroyed, because our past wars were waged with animals; now we have wars with the Venetians and the Turks of the Sultan. And as regards the King of Cochin, I have already written to your Highness that it would be well to have a strong castle in Cranganore on a passage of the river which goes to Calicut, because it would hinder the transport by that way of a single peck of pepper. With the force we have at sea we will discover what these new enemies may be, for I trust in the mercy of God that He will remember us, since all the rest is of little importance. Let it be known for certain that as long as you may be powerful at sea, you will hold India as yours; and if you do not possess this power, little will avail you a fortress on shore; and as to expelling the Moors (Muhammadans) from the country, I have found the right way to do it, but it is a long story, and it will be done when the Lord pleases and will thus be served.'