It being now noon, and thinking that the people staid too long on shore as they went off before day-break, the admiral began to suspect that some misfortune had befallen them either by land or sea; but not being able to see the hermitage from the place where he then lay, he sailed round a point which intervened, and then saw a multitude of people on horseback, who dismounted and went into the boat to attack the caravel. Suspecting what had really happened, the admiral ordered all his remaining hands to quarters well armed, but made no shew of resistance that the Portuguese might come near. When they were near the admiral, the chief man among them stood up and demanded a parley, which the admiral agreed to in hope that he might come on board and might be secured without any breach of faith, considering that he had seized the Spaniards without any just cause. But the Portuguese would not venture nearer than was sufficient for being heard; whereupon the admiral told him that he was surprised at his irregular proceedings, and that none of his men had come off in the boat, since they had gone ashore upon assurance of safety and offers of assistance, and more especially as the governor of the island had sent to welcome him. He desired him to consider that their conduct was contrary to the laws of honour, such as even enemies would, not have been guilty of, and at which the king of Portugal would be highly offended; since when any of his subjects landed in the dominions of their Catholic majesties or resided there, even without any safe conduct, they were perfectly safe and were treated with all manner of civility. Besides, he declared that their Catholic majesties had given him letters of recommendation to all princes potentates and other persons in the world, which he was ready to shew if he would come on board; and as such letters were received in all places with respect, and he and the subjects of their Catholic majesties always well treated on their account, much more ought they to be so in the dominions of Portugal, their sovereigns being such near neighbours and allies; and as he was their great admiral of the ocean and viceroy of the Indies which he had discovered, he was ready to shew him all this under their highnesses hands and seals. Accordingly at that distance he exhibited his commissions, and told him he might draw near without any apprehension, as he was commanded to pay the utmost civility to such Portuguese ships as he might fall in with. He added, that even if they should persist in detaining his men, this should not prevent his return to Spain, as he still had a sufficient number, not only to return to Seville, but if need were to punish his treacherous conduct which he well deserved; besides that he would be assuredly punished by his own king, for giving a cause of war between Spain and Portugal.
The Portuguese captain and his men made answer, that they neither knew their Catholic majesties or their letters, neither did they fear them, and would make him to know what Portugal was. From this answer, the admiral suspected that some breach had occurred between the crowns since his departure, and therefore gave him such an answer as his folly deserved. At last when about to depart, the captain stood up and said that the admiral might go with his caravel to the harbour, as all he had done was by order of the king his master. The admiral desired all his ships company to bear witness to this, and then calling out to the Portuguese, declared he would not leave his caravel till he had taken an hundred Portuguese to carry prisoners to Castile, and that he would utterly destroy the whole island. This said, the Portuguese went away to the land, and the admiral came to anchor in the port where he had first arrived, being obliged by the wind to do so. But the wind increasing next day and the place being unsafe, he lost his anchors and was obliged to stand out to sea towards the island of St Michael; resolving, in case he might be unable to come to anchor there, to stand out to sea notwithstanding the danger, and that he now had only three able seamen left and some grummets, all the rest of the crew being landsmen and Indians who knew nothing of sea affairs. Supplying the want of the absent hands by his own continual personal attention, he passed the whole of that night in much danger and anxiety, and when day appeared he perceived that the had lost sight of the island of St Michael. The weather being now calmer, he resolved to return to St Mary that he might endeavour to recover his men, anchors, and boat.
On Thursday the twenty-first of February in the afternoon he got back to the island of St Mary, and a boat soon afterwards came off with five men and a notary, who all came on board upon assurance of safety, and staid all night, it being then too late to return safely to the shore. Next day the notary declared that they came from the governor to be certainly informed whence the ship came, and whether it had a commission from their Catholic majesties, and that being fully satisfied on these points the admiral might depend upon receiving every friendly assistance; but all this was merely because they could not succeed in seizing the ship and the admiral, and were therefore afraid of the consequences of what they had already done. The admiral suppressed his resentment and thanked them for their civil offers; and since they now proceeded according to the maritime rules and customs, declared his readiness to satisfy them. He accordingly shewed them the letters of their Catholic majesties directed to all their own subjects and to those of other princes, and his own commission for the voyage; upon which the Portuguese went on shore quite satisfied, and soon dismissed the Spanish boat and all the seamen. From them the admiral learnt that it was reported in the island, that the king of Portugal had sent orders to all his subjects to secure the person of the admiral wherever he might be found.
The admiral sailed from the island of St Mary for Spain on Sunday the twenty-fourth of February, being still much in want of wood and ballast, which he could not take in because of the badness of the weather; but the wind being fair he was unwilling to make any longer delay. Being about 100 leagues from the nearest land, a swallow came on board the ship, driven out to sea as was believed by a storm; and this was the more probable as a great many more swallows and other land birds came onboard next day, the twenty-eighth February, and a whale was seen. On the third of March about midnight it blew so great a storm as to split their sails; and being in great danger of perishing, they made a vow to send one of their number on a pilgrimage to the shrine of Neustra Senhora de Cintra at Guelva, and the lot fell again on the admiral, shewing that his offerings were more acceptable than those of others. While thus driving on under bare poles, amid high winds, a raging sea, and frightful thunder and lightning, it pleased God to give them a sight of land about midnight. But this threatened them with new danger; and to avoid being beaten to pieces on the rocks, or running into some unknown place whence they might not be able to get off, they were under the necessity to make some sail and to beat up against the storm till day. When day appeared they found themselves close in with the rock of Lisbon, and were forced to put in there for present safety. The people and seamen of that country were much astonished at the news, and flocked from all parts to behold the wonder; for such they considered a ship which had escaped so terrible a storm, as they had heard of many vessels having perished about the coast of Flanders and other parts at this time. The admiral came to anchor in the river Tagus on Monday the fourth of March, and immediately sent off an express to their Catholic majesties with an account of his arrival, and another to the king of Portugal asking leave to come to anchor off the city of Lisbon; for he did not consider himself in safety where he then lay, especially from any that might entertain evil designs against him, who might believe that in destroying him they did acceptable service to their own king by obstructing the success of the court of Spain.