Don Alexius de Menezes archbishop of Goa went about this time to visit the Christians of St Thomas, who lived dispersedly in the mountains of Malabar, in Muli, Turubuli, Maota, Batimena, Diamper, Pimienta, Tetemute, Porca, Paru, and Cartuti. These Christians continued stedfast at the faith till about the year 750, yet with some tincture of error. About the year 810 the second Thomas, formerly mentioned, came to this country, where he repaired the churches that had been erected by the apostle and restored the true doctrine; but about the year 900 this church was overrun by the Nestorian heresy. In the year 890 two Chaldeans came here from Babylon, named Mar Xarsio and Mar Prod, who divided the district into two bishoprics, and were ever afterwards prayed to as saints, till our archbishop ordered this to be discontinued, as he much suspected they had not been legitimately canonized. After these Chaldeans came one Mar Joanne, who was sent by the Greek Patriarch, and resided at Cranganor where he introduced the Chaldean ritual. His successor was Mar Jacob, who died in 1500, and was succeeded by Mar Joannato. Thus the bishops and heresies continued among the Thomists till 1536, when Pope Paul IV. appointed Juan Bermudez patriarch of Ethiopia, Simin Sulacca bishop of Caheremit the metropolis of Mesopotamia, Mar Elias as patriarch of Mosul, and Mar Joseph bishop of Nineveh, whom he ordered to govern the Christians of Malabar, with the bishop Ambrose Montecelli for his coadjutor. By this interference of the Pope there were two patriarchs of the East, one orthodox at Mosul, and the other heretical at Antioch. Joseph and Ambrose went over to the mountains of Malabar, to assume the pastoral charge of the Thomists; but the latter separated from the former and went to Goa, where after reading divinity for some time he died at Cochin in the year 1557. As Don George Temudo bishop of Cochin perceived that Joseph spread the poison of Nestorius among his flock in Malabar, he contrived to have him apprehended and sent in chains to Portugal, were he was permitted to return to his bishopric on promise of amendment420. On his return he found Mar Abraham officiating as bishop of the Thomists, who had chosen him in the absence of Joseph; and as Abraham found himself persecuted, or disturbed in the exercise of his functions by Joseph, he went to Rome where he got a brief from Paul IV. appointing him bishop of the Thomists, having engaged to reduce that people to the orthodox faith. Yet neither he nor Joseph adhered to their engagements, but continued in their heresies. After this one Mar Simon came to Malabar, saying that he was sent by the patriarch of Babylon to officiate as bishop of Malabar. He was received by the queen of Pimienta and placed at Cartuse, where he exercised episcopal functions; till being carried to Lisbon he was sent thence to Rome, where he was condemned by Pope Sixtus Quintus as a mere Nestorian and not even a priest. After the death of Mar Abraham his archdeacon governed the diocese, as no Babylonian prelates dared to come to Malabar, Don Alexius, the archbishop of Goa, using his utmost endeavours to keep out all such heretical prelates, which was the particular occasion of his present visitation.

This prelate found that, among other errors, the Thomists denied the virginity of our blessed lady421: They rejected the use of images: they believed the souls of the just did not enjoy the beatific presence of God till after the general judgment: they allowed only of three sacraments, baptism, ordination and the eucharist: instead of confession they used perfuming in their churches: the wine employed in the sacrament was made from cocoas: their host was a cake made with oil and salt: their priests were ordained at seventeen years of age, and were permitted to marry after ordination: fathers, sons, and grandsons administered the sacrament in the same church: the Catatorias or Caffaneras, so they called the wives of priests, wore a distinguishing mark to be known by: in matrimony, they used no other formalities except the consent of parties and consummation: the women observed the time prescribed by the law of Moses in regard to churching: no sacraments were administered gratuitously: holy water was mixed with some powder of frankincense, and some of the soil on which St Thomas was supposed to have trodden: they used sorcery and witchcraft: In fine, that all was error, confusion, and heresy.

Don Alexius with much labour and toil convinced them of their errors and converted them to the true faith, so that whole towns were baptised and reconciled to the Roman see. He even held a provincial synod at Diamper, all the decrees of which were confirmed by the Pope; and Francisco Rodriguez, a Jesuit who had assisted the archbishop on this important visitation, was made bishop of that diocese. On the breaking up of the synod, Don Alexius visited all the churches in these parts. While in the country of the queen of Changanate, visiting the church of Talavecare, one of the most ancient in those parts, they shewed him three plates on which were engraven certain privileges and revenues granted by the king of Ceylon, at the time when the Babylonians Zabro and Proo422, were in that country. At this place likewise Don Alexius met Topamuta Pandara, king of Gundara423 in the neighbourhood of Changanate, to whom he presented a letter from king Philip giving him the title of brother, for having allowed liberty for the exercise of the Christian religion in his dominions424.

In the year 1596, a Moor, named Pate Marcar obtained leave from the zamorin to build a fort in the peninsula of Pudepatam, 77 leagues from Goa and 33 from Cochin, where was a most convenient station for piratical paraos, to annoy the trade of the Malabar coast; and having built a square fort at this place, he went thither with all his kinsmen and followers, and did much injury to the Portuguese and their allies, even making incursions upon their maritime possessions, whence, on several occasions, he carried off much spoil. Pate Marcar soon died, and was succeeded in the sovereignty of the fort by his nephew Mahomet Cuneale Marcar, who added greatly to the strength of the fort; and foreseeing that the Portuguese might seek to be revenged for the injuries they had sustained, he fortified the town both by sea, and land, which he named Cuneale after himself. On the land side he made a deep ditch with a double wall above seven feet thick, flanked at regular distances with towers called zarames, all of which were mounted with small cannon. Between the two creeks forming the peninsula, he built a strong wall with two towers to secure the town, and lined the sea-shore with strong palisades; flanked by two bastions, one of which considerably larger than the other, was mounted with heavy cannon to defend the entrance of the harbour, which was farther secured by a boom of masts strongly chained together. Having thus, as he thought, provided a secure retreat, he continued his uncle's enterprises against the Portuguese with much success, assisting all their enemies against them, even robbing the Malabar traders on the coast, and filled his residence with rich plunder. The viceroy Albuquerque had endeavoured to destroy this nest of pirates, so prejudicial to the Portuguese trade, and had even prevailed on the zamorin to concur in the destruction of Cuneale, so that a treaty had been entered into, by which the zamorin engaged to besiege Cuneale by land, while the Portuguese fleet attacked him by sea. Both parties provided according to stipulation for this joint expedition; but it was postponed for some time, in consequence of the change in the government by the arrival of the Count of Vidigueyra as viceroy, and even by the secret concurrence of the zamorin in the piracies of Cuneale, who communicated to him a share of the plunder.