Cuneale was so much elated by his success in repelling the Portuguese, that, in addition to his former title, he stiled himself Defender of the Mahometan Faith and Conqueror of the Portuguese; but when the season returned for maritime operations on the coast, the viceroy sent Andrew Furtado against him with three gallies, 54 other vessels, and a powerful military force. In the mean time Antonio de Noronha continued to blockade the port all winter, taking several vessels laden with provisions, and on different occasions slew above 100 Moors who opposed him in taking fresh water for his ships. While on his way from Goa, Furtado dissuaded the rajah of Banguel and the queen or rana of Olala from sending aid to Cuneale as they intended, and cut off five ships from Mecca that were going with relief to the enemy. When Furtado came to anchor in the port of Cuneale, he sent to treat with the zamorin, who had continued the siege on the land side all winter according to his engagement, and an interview took place between them on the shore where the zamorin came to meet him. The zamorin was naked from the waist upwards. Round his middle a piece of cloth of gold was wrapped, hanging to his knees and fastened by a girdle of inestimable value, about the breadth of a hand. His arms were covered from the elbows to the wrists with golden bracelets adorned with rich jewels, and so heavily laden that two men supported his arms. He wore an extraordinarily rich chain about his neck, and so many diamonds and rubies hung from his ears that they were stretched down almost to his shoulders by their weight. He seemed about 30 years of age, and had a majestic presence. A little on one side stood the prince, carrying a naked sword. Behind him were many of his nobles; among whom was father Francisco Rodriquez, the new bishop of the Thomists in Malabar. The zamorin and Furtado embraced in token of friendship, on which all the cannon in the fleet fired a salvo. After this friendly meeting they retired into the tent of the zamorin, where they had a long conference about their future operations; and on taking leave, Furtado put a rich collar about the neck of the zamorin, and they parted in a most amicable manner.

The rajah of Tanor and other great men were sent by the zamorin on board the admiral ship, having full powers from their sovereign to treat and conclude on all things concerning the joint interests of both parties, and every thing was settled to mutual satisfaction. There now arrived from Goa and other places, a galley and galleon, with 11 ships and 21 smaller vessels, bringing ammunition and 790 soldiers, upon which Furtado commenced the active operations of the siege, raising entrenchments and batteries, and taking absolute possession of every avenue leading to the fort and peninsula by water. He likewise caused some advanced works belonging to the enemy to be assaulted, on which Cuneale came in person to assist in their defence, and for a time repulsed the assailants, till Furtado landed with a reinforcement, on which the Portuguese remained victorious, slaying 600 of the Moors, with the loss of two officers and nine privates on their side. Fort Blanco or the white tower was next assaulted, but with more bravery than success. Yet Cuneale seeing that he could not much longer hold out, offered rich presents to the zamarin to admit him to surrender upon security of his own life and the safety of his garrison. But on this secret negociation coming to the knowledge of Furtado, he made a furious assault on the works, which were at the same time assailed on the land side by 6000 Nayres, by which joint attack the lower town or petah was taken, plundered, and burnt. Batteries were immediately erected against the upper town and fort, and as their fire soon ruined the defences, Cuneale was constrained to surrender at discretion, merely bargaining that his life should be saved. He accordingly marched out having a black veil on his head, and carrying his sword with the point downwards, which he surrendered to the zamorin, who immediately delivered it to Furtado. According to one of the articles of agreement the spoil was to have been equally divided; but Furtado dealt generously by the zamorin, alleging that this was to be understood only in respect to the artillery, and appeased his own soldiers who expected that reward of their labour. The fort and all other works were levelled with the ground, and Furtado returned with the fleet and army to Goa.

Cuneale was about 50 years of age, of a low stature, but strong and well made. He and his nephew Cinale, with other forty Moors of note, were sent as prisoners on board the fleet, where they well treated; but as soon as some of them were set on shore at Goa, they were torn in pieces by the rabble; and Cuneale and his nephew were both publicly beheaded by order of the viceroy, so that the government and the mob went hand and hand to commit murder and a flagrant breach of faith. How can those who are guilty of such enormities give the name of barbarians to the much more honourable Indians!

In the year 1600, Ayres de Saldanna arrived at Goa as viceroy to supersede the Count de Vidugueira, who was universally disliked by the Portuguese inhabitants. The marble statue of the great Vasco de Gama, his grandfather, stood over the principal gate of the city, fastened to the wall by a strong bar of iron. At the instigation of some enemies to the count, a French engineer named Sebastian Tibao applied to the iron bar during the night a certain herb that has the quality of eating iron, so that the statue fell down next night, and its quarters were hung up in different parts of the city. On the day when the count was to embark for his return to Portugal, a party of armed men went on board before him, and hung up his effigy at the yard arm, made exactly like him both in face and habit. Just as he was going on board they returned; and on seeing the effigy he asked what it was, when someone answered, "It is your lordship, whom these men have hung up." He made no reply, but ordered the figure to be thrown into the sea and immediately set sail; but two days afterwards had to return to port for a new stock of fowls, as all these he took with him were poisoned. He was better beloved by the elements than by those whom he had governed; for he went all the way from India to Lisbon without once needing to furl a sail. By the constant chafing of the yards on the masts, it was found impossible to lower the yards in the usual way when the ship arrived at Lisbon, insomuch that they had to be cut down. Sailing from Goa on the 25th December 1600, he arrived at Lisbon on the 27th May 1601, having spent only five months on the voyage.

During the administration of Ayres de Saldana, Xilimixa king of Aracan, who had possessed himself of the kingdom of Pegu, gave the port of Siriam to the Portuguese in grateful acknowledgment of their services. That town and port is at the mouth of the river Siriam which flows within a league of the city of Bagou, the capital of Pegu. This grant was obtained by Philip Brito de Nicote, who proved false and ungrateful to the king of Aracan, who had raised him from the lowest rank to his favour and esteem. By his persuasion, Xilimixa erected a custom-house at the entry to the river Siriam to increase his revenues; which Brito meant afterwards to seize, and to build a fort there, on purpose to give a footing for the Portuguese to conquer the kingdom. Xilimixa accordingly built the custom-house, which he gave in charge to one Bannadala who fortified himself and suffered no Portugeuse to enter there, except a Dominican named Belchior de Luz. Nicote, seeing his purposes likely to be defeated by Bannadala, determined to gain possession by force before the works were completed. He had along with him at this time three Portuguese officers and fifty men, whom he ordered to surprize the fort and turn out Bannadala, trusting to his great credit with Xilimixa to bear him out in this procedure. The Portuguese officers accordingly executed their orders so effectually, that they used to be called the Founders of the Portuguese dominion in Pegu, and Salvador Ribeyro their commander was like to have got the whole credit of the exploit, as some even affirmed that he was its author, though in reality all was due to Nicote. Bannadala being expelled from his fort, fortified himself with 1000 men in a neighbouring island of the river Siriam, and seized the treasures of the pagoda of Digan to maintain his troops. Xilimixa was much offended by the conduct of the Portuguese in this affair, and resolved to support Bannadala, but was dissuaded by the contrivances of Nicote, who represented that he was about to favour a sacrilegious robber, and offered to arrange matters with the Portuguese to his entire satisfaction. He accordingly went to Siriam, where he ordered every thing to his own mind; and when the fort was nearly finished, he went to Goa, where he offered to deliver up the fort to the viceroy, whence the Portuguese might easily conquer the kingdom of his master, to whom he represented his voyage to Goa as intended to procure an auxiliary force which would enable him to make a conquest of Bengal. At the same time Nicote negociated with all the princes in the provinces adjoining the dominions of Xilimixa, persuading them to confederate with the Portuguese viceroy, by which means they might easily conquer the kingdom of Pegu; and several of them sent ambassadors along with him to Goa for this purpose.