In the course of the full day which they spent on the island the men found the village completely deserted. The church and the friars' house were burned almost to the ground. In the mission that for years had been tended by the sons of St. Francis, signs of desolation reigned everywhere.

Near the entrance to the church two graves were discovered, one of which was only partially covered with earth. In each of the graves there was a badly abused corpse, which the soldiers were able to identify as the bodies of Fray Miguel de Añon and Fray Antonio de Badajoz, the two friars stationed at the doctrina on Santa Catalina at the time of the Revolt. Both bodies had been mutilated: their arms and legs had been broken in four places, and their legs tied together. Close to one of the graves, half-buried in the ground, was the severed head of Fray Miguel, along with some small bones. Stark evidence was seen of severe blows from a tomahawk, which had resulted in the cracking of his skull and the spilling of his brains as the definitive cause of his death.

The bodies were already in an advanced stage of putrefaction, and this ruled out the possibility of their being taken at that time to San Agustin. The two corpses were then reburied in a decent manner at the foot of the large cross which Fray Miguel had erected. A modest marker was placed at the graves, so that at a later date they could readily be found. The soldiers did, however, take with them the severed head of Fray Miguel, and also some small bones from his body.

That same evening crossing back to where, outside Tolomato, the Governor and his force were preparing to set sail, Sargento Diaz gave Don Gonzalo a verbal report (made official by a scribe) of their findings. The subaltern official likewise gave the Governor the precious relics of Fray Miguel's body which he had brought from the island, and these Don Gonzalo in turn handed over to Fray Blas.¹¹

About six years later – in 1603, as Oré implies,¹² or in 1605, as Barcia in his Ensayo Cronológico explicitly says¹³ – the Spaniards exhumed the two bodies and brought them to San Agustin. Where precisely in the mission compound these relics of the Servants of God were kept has not been ascertained. Significant modifications in the organization of the convento and in the life of the friars must have been introduced when, in 1606, the mission status was changed to that of a custody, implying a more stabilized form of community life and a more formal system of governance. An even more significant development took place after 1612, when the General Chapter of the Franciscan Order, held in Rome, decreed that the Custody of Santa Elena should be elevated to the status of a province under the same title. At that time, the principal convento in La Florida, "La Concepción" (sometimes also called "San Francisco"), became the house of novitiate. As such, it would have been a place of special recollection and prayer, a friary for the training and inspiration of novices. Presumably the relics of the Servants of God kept there would have received particular attention and been the object of singular devotion in the religious house which was at once the head and the heart of the first province of the Franciscan order established in the territory of the future United States of America.

No record is known to exist which would indicate where within the area of the friary compound these precious relics of the martyrs were kept. The manner of their custody would be a determining factor – perhaps the single most important factor – in locating these relics today. Theoretically there are two possibilities of what took place. The first possibility – the less likely, it would seem – is that the bones were interred in the camposanto. In that case it is less probable– though not impossible – that the departing friars in 1763 would have disinterred the relics in order to transport them to the friars' place of refuge in Cuba. Should this, the less likely possibility, be the course that was actually followed, then the chances of discovering and unearthing the bones are not very real. For seemingly, the ancient cemetery is now, perhaps irreversibly, part of the macadamized parking lot for the Florida State Barracks which occupies the old Franciscan site.

The second possibility – and the one which would seem to offer the greater probability that these relics of the martyred friars might yet be discovered – is that the religious community at the headquarters of the Province of Santa Elena had determined to keep them above ground. In the area of the church or convento, in some sort of movable receptacle, such as a strongbox, the relics might have been kept with reverence and some outward display of honor and respect. In such a case, when in 1763, with the ceding of Spain's rights in La Florida to Britain, the friars definitively left San Agustin, they could readily have taken the box with them to Cuba.

If the bones were in fact kept in a sort of casket above ground – and we do not know whether they were or not – the receptacle could quite conveniently have been taken to Cuba by the departing friars. A search there for the relics remains a possibility. The Cause is interested in pursuing the search further and has taken initial steps toward investigating the matter.