Having established all things to his mind, the admiral left Don Peter Margarite, a gentleman of Catalonia, as governor of the fort, with a garrison of fifty-six men, and returned himself to Isabella, where he arrived on the 29th of March. He here found matters much worse than at his departure, only seventeen days before. Many of the colonists were dead, and great numbers sick, while those who were still in health were quite disheartened at the prospect of following the fate of their companions. The provisions which had been brought from Spain were growing extremely scarce, owing to a great quantity of them being spoiled through the negligence of the sea captains, while such as had been landed in good condition would not keep long, on account of the dampness and heat of the climate. All were therefore on short allowance, and the flour they had still in store being near spent, it became necessary to construct a mill for grinding corn: But, as all the labouring people were sick, the better sort were forced to work, which was extremely grievous to them, especially as they were in want of food. In this emergency the admiral was under the necessity to use compulsion for carrying on the public works, that the people might not perish. This rendered him odious to the leading Spaniards, and gave occasion to Friar Boyle to charge him with cruelty; though it has been alleged that the true cause of his aversion to the admiral proceeded from being refused a larger allowance for himself and his servants than was given to others. Provisions became at length so scarce, that even the sick were often reduced to one egg each, and a pot of boiled Spanish pease among five. The want of proper medicines added greatly to the distress; for though some had been brought along with the expedition, they did not agree with all constitutions; and, what was still worse, they had no medical person to attend upon the sick. Many well-born men, who had never been accustomed to such hardships, being sick and starving, and without all hope of relief, sunk under their situation, and died almost of despair. Afterwards, when the town of Isabella was abandoned, it was currently reported that dreadful noises were heard in the place, so that for a long while no one durst venture to go that way.

To add to his affliction, the admiral received intelligence from Fort St Thomas, that all the Indians had abandoned their towns, and that Caunabo, the cacique of one of the provinces, was making preparations to reduce the fort. The admiral sent immediately a reinforcement of seventy of the healthiest of his men to the fort, escorting some beasts of burden, laden with arms and provisions. He likewise ordered Alonso de Ojedo to take the field with as many men as were able to march, leaving only the sick and the mechanics behind; desiring him to march about the country, particularly the Royal Plain, where there were many caciques and an innumerable multitude of Indians; intending to intimidate the natives by a display of the Spanish force, and to accustom the Spaniards to use the provisions of the country, as their own were nearly spent. Ojeda left Isabella with above 400 men on the 9th of April; and as soon as he had passed Golden River in the Royal Plain, he seized the cacique of one of the towns, with his brother and nephew, whom he sent prisoners to Isabella, and caused the ears of an Indian to be cut off in the market place. The reason of this severity was, because when three Spaniards were going from Fort St Thomas to Isabella, the cacique gave them five Indians to carry their baggage across the river, who left the Spaniards and carried the baggage back to the town, for which the cacique was so far from punishing them, that he detained the baggage. The cacique of another town, on seeing these chiefs carried away prisoners, went along with them to Isabella, believing he might be able to procure their pardon from the admiral, as he had always been friendly to the Spaniards. "As soon as they arrived, the admiral ordered their heads to be cut off in the market-place, a crier proclaiming the offences for which they were to suffer this condign punishment; but for the sake of the friendly cacique he forgave them124." About this time a horseman came to Isabella from the fort, who reported that the inhabitants of the town belonging to the cacique who was their prisoner had beset five Spaniards with intention to put them to death; but that he and his horse had rescued them from above 400 of the natives, who all fled before him out of fear for his horse, and that he had wounded several of them with his lance.

Having pacified the threatened commotions to all appearance for the present, the admiral determined to prosecute his maritime discoveries as he had been directed by their Catholic majesties, and because his disposition was averse from idleness, and much inclined to explore the country which he had discovered. For the better government of the colony during his absence, he appointed a council, of which his brother Don James Columbus was constituted president; the other members were, Friar Boyle, Peter Fernandez Coronel, the chief alguazil or judge, Alonso Sanchez de Carvajal, and John de Luxon. Don Peter Margarite was ordered to continue marching up and down the country with the military force, being above 400 men; and the admiral left such instructions for the good management of the colony in his absence as he deemed convenient and necessary.

Leaving two vessels in the harbour of Isabella to serve the colony in any case of emergency, the admiral set sail on Thursday the 24th of April 1494, with one large ship and two caravels. Taking his course to the westwards, he proceeded to Monte Christo and the harbour of Nativity, where he inquired for Guacanagari, who happened to be absent; and although his people said he would be soon back, the admiral was unwilling to delay his voyage. He then advanced to the isle of Tortuga, but was forced back by contrary winds, and came to anchor in a river which he named Guadalquivir. On the 29th of April he reached Port St Nicholas, whence he discovered the eastern point of the island of Cuba, called Bayatiquiri by the natives, but which he named Cape Alpha and Omega125. Crossing the strait between Hispaniola and Cuba, which is eighteen leagues broad, he began to explore the southern coast of Cuba, where he discovered a large bay, which he named Puerto Grande126, or Great Harbour, the mouth of which is an hundred and fifty paces wide. He came to anchor here, and procured considerable quantities of fish, brought by the Indians in canoes. On Sunday the 7th of May he proceeded along the coast, which he found everywhere provided with excellent harbours, high mountains, and numerous rivers. As he kept everywhere as close as possible to the shore, infinite numbers of Indians resorted continually to the ships in their canoes, supplying the Spaniards freely with provisions, under the idea that they were come from heaven: on these occasions the admiral always gave them toys, with which they went away perfectly satisfied.

He now returned towards the south-east, on purpose to explore another island named Jamaica, which some believe to have been the place so frequently mentioned by the Indians of Lucayo, under the name of Babeche or Bohio. He accordingly reached the coast of Jamaica on Monday the 14th of May, and thought it the most beautiful of all the islands he had yet seen, and from it great numbers of canoes came off to the ships; yet on sending the boats to explore and sound a port, a great many armed canoes interposed to hinder the Spaniards from landing. The admiral therefore made sail towards another place, which he named Puerto Bueno, or the Good Harbour, where a similar opposition was made by the natives. Irritated by this unfriendly reception, the admiral ordered a flight of arrows to be discharged among the Indians from his cross-bows, by which six or seven of them were wounded, after which the rest of the natives came peaceably to the ships. Next Friday, being the 18th May, he sailed along the coast to the westwards, so near the shore that many canoes continually followed the ships, bartering such things as they possessed for any baubles given them by the Spaniards. The wind being always contrary, the admiral resolved to return to Cuba, that he might satisfy himself whether it were an island or continent. At this time an Indian youth came on board, and expressed by signs an anxious desire to go along with the Christians; and though his parents and friends entreated him with tears not to leave them, he would not be prevailed on to stay, but went and hid himself in a private part of the ship, to avoid their importunity.