Matters reached their climax in the matter of further fortifications. Osorio wanted to build a sea wall in front of the city, such as the engineer Sanchez had planned years before, at the beginning of Mazariegos's administration. Menendez curtly dismissed that scheme, and commissioned his son-in-law, Pedro de Valdes, with some other officers from Florida, to survey the waterfront of the city and recommend additional fortifications. They reported that it would be folly to build a sea wall, and that all that was needed was a round tower, about thirty-seven feet high, on the headland opposite the Morro, on which latter an observation tower had already been erected. Valdes suggested that the tower might be built by the garrison of La Fuerza, at no cost, if the governor would provide the materials. This Osorio refused to do. He had no money for such a purpose, and no authority to spend any for it. Moreover, he condemned the plan of thus dividing the garrison, holding that it would be far better to finish La Fuerza and concentrate all the forces there. The outcome of it was, therefore, that the proposed Punta Castle had to be for the time abandoned; Menendez perforce contenting himself with some earth-works on Punta, in which he placed a couple of cannons.

At the same time other friction arose at Santiago, a place which could not yet be altogether neglected. Menendez's attention was called to that place by having one of his own ships chased into Santiago harbor by a French privateer. The captain of that ship reported to him that Santiago had a fine harbor but practically no defences. A fort had indeed been begun on the headland at one side of the harbor entrance, but had not been finished, and the sea wall for which the people had petitioned had not been started. Menendez thereupon sent thither a company of fifty men with four cannon, under command of Captain Godoy; without, of course, consulting Osorio as governor of the island.

This force remained there about three months, in the summer of 1567. It saw nothing of French privateers, or of any menace of an attack upon the town. But it did see a good deal of merchant ships of various nations, French, Scottish and Portuguese, which came thither with slaves and merchandise, but which seldom ventured in for fear of Godoy and his men. For such trade with foreigners, and particularly with those who were or were suspected to be heretics was strictly forbidden. Godoy and his men were therefore most unwelcome visitors, to the merchants and people of Santiago, and to the lieutenant of the governor, Martin de Mendoza. It was suspected, not without reason, that Osorio had sent word to Mendoza to antagonize Godoy as much as possible. At any rate, one day a particularly big French merchant vessel came into the harbor; Godoy rallied his men to the battery near the wharf, to prevent it from landing its cargo; and Mendoza arrested Godoy and sent him to jail, where he kept him until the cargo had been discharged and another taken on in its place, amid the jubilations of the people. Then Godoy was released, with profound apologies for the error which had been committed in arresting him!

Godoy remained for some time thereafter at Santiago, though much against his will. His superior officer commanded him to remain. But he sent an appeal for relief to the Supreme Court of Hispaniola, with the result that Mendoza was removed from office, in the winter of 1557-58. This was a relief to both Mendoza and Godoy, though it did not make their feelings less bitter. On Palm Sunday the two met at church, Mendoza accompanied by his wife and Godoy by a friend named Cordoba. The latter two grossly insulted both Mendoza and his wife, then ran into the church for security from chastisement, forcibly resisted arrest, and committed acts of sacrilege. They were finally overpowered, and on being brought to trial before the local court were condemned, Godoy to be hanged and his body quartered, and Cordoba to be flogged and sent to the galleys. The sentence was executed, Godoy being hanged on a gallows at the door of the church the sanctity of which he had violated. When Menendez heard of this he was furious. He instituted proceedings against Mendoza and the local alcaldes at Santiago, charging them with conspiracy to destroy Godoy so that their illegal traffic with Frenchmen and other foreigners would not be molested. Mendoza thought it prudent to remove to Carthagena, in New Granada, for fear of personal violence; whence he proceeded to Spain, where he was acquitted of all the charges which Menendez had made against him.

Meantime, the governorship of Osorio had ended. Early in 1567, at the time when the controversy arose over the sea wall and the Punta fortifications, he had realized that his usefulness as governor was ended, and had asked the King to accept his resignation; declaring that his presence there was no longer of value to his majesty. In August, 1567, the King appointed Diego de Santillan to be governor in his stead, and commissioned him to investigate Osorio's stewardship, and particularly to bring him to trial on certain charges of false arrest and cruelty to a prisoner. But just as Santillan was about to embark for Cuba, in October, 1567, his commission was revoked and Menendez was appointed governor of Cuba in his stead. It has been said that this appointment was made by the fanatical King to show his approval and appreciation of Menendez's act on September 20, 1565, when he massacred the French garrison of Fort Caroline, Florida, "not as Frenchmen but as Lutherans."

Menendez was not able, however, as Adelantado of Florida, to reside permanently in Cuba, or indeed to spend much time there; wherefore it was arranged that a lieutenant governor should be the actual administrator in his stead. The man chosen was Francisco Zayas, a lawyer, who had been selected by the King to be lieutenant governor with Santillan. He reached Havana in July, 1568, and at once assumed the office which Osorio was glad to relinquish. It cannot be said that he was greatly welcomed by the people of Havana or of any part of Cuba, since it was assumed that he would be a mere puppet acting for Menendez, and it was feared that Menendez would use Cuba as a mere stepping stone or adjunct to Florida, draining it of men and resources for the benefit of the larger province on the continent. This apprehension, happily, was not realized.

Osorio personally had cause for fear. Zayas was commissioned to conduct the investigation into his affairs, and there was every reason to suppose that Menendez would compel him to make the inquest as drastic as possible and to impose the heaviest possible penalties for any misdemeanors which might be proved against him. But Zayas was after all a just and reasonable man, who was not afraid to assert his independence of Menendez, particularly since, as he pointed out, his commission as lieutenant governor antedated that of Menendez as governor by two months. Moreover the people of Havana, through dislike of Menendez and fear of his policy, gave their strongest support to Osorio, testifying in his behalf, and at the end sending a great memorial to the King, signed by almost every man of consequence in Havana, petitioning for the utmost possible favor for the governor. The result was that the lightest of sentences was passed upon Osorio, two years after his actual retirement from office.

In dealing thus with Osorio, however, Zayas sealed his own fate. Nothing that he could do thereafter pleased Menendez, while he was called upon by the latter to do or to sanction things which offended his sense of right. By the beginning of May, 1569, relations between them reached the breaking point. Menendez caused the city council to protest that Zayas had never filed the bond which was required of a lieutenant governor, and to characterize this as a grave offence, indicating criminal intent. Zayas thereupon resigned his office. Suits were instituted against him and his wife in Spain, by Menendez, and he returned to the country to meet them. He appears to have been successful in his defence, since the King subsequently appointed him to be a judge in the Canary Islands.

Menendez appointed in place of Zayas as lieutenant governor Diego de Cabrera, who had filled that place under Osorio. His term of service was short, however, and no fewer than five others succeeded him, one after another, during the administration of Menendez. They were Diego de Ribera; Pedro Menendez Marquez, a nephew of Menendez; Juan de Ynestrosa; Juan Alfonso de Nabia; and Sancho Pardo Osorio.

Diego de Ribera, who served for a brief space under Menendez as lieutenant-governor, was captain of the galleons, and was presently commissioned for an expedition to Florida. He was succeeded by Pedro Menendez Marquez, a nephew of Menendez. He was an accomplished navigator and on that account was directed by his uncle to sound and chart the Old Bahama Channel, a much-frequented route of commerce and approach to Cuba from the north and east. To this undertaking he devoted only a few weeks, but his observations were so exact, thorough and comprehensive that the Council for the Indies, on receiving his charts, immediately approved them and ordered them to be regarded as the authority for navigation of those waters.