
With the arrival of the Portuguese in the 16th century in South India, the ancient church of St. Thomas for the first time began to undergo the decisive effect of the Portuguese colonial era coupled with the adverse effects of Roman Catholicism. As a result, it was forced to succumb under Rome through the Portuguese. Five well-planned maneuvers were used to force this church finally to obey Rome: bringing the church of Thomas under the administrative control of the Portuguese; subjecting it to thorough latinization by establishing two clergy training institutes; forcefully terminating all contacts with the East Syrian Church; forcing the whole Church through a representative assembly to go under Rome; and imposing the direct rule of the Roman Catholic regime while destroying the precious indigenous heritage of the Church of St. Thomas.
The Thomas Christians as a whole reacted against Roman Catholicism in 1653 through the famous Coonan Cross Oath. Although the event was a great success, the Church of St. Thomas could not continue for long in its determination. As pressures from the Roman Catholic side continued, the leadership became subject to division. A group once again rejoined Roman Catholicism and stood against the aspirations of the people who stood for freedom from Rome; the latter group later became the Orthodox Church of India.
When the Portuguese landed in India, they met the Christians of St. Thomas and felt satisfied that their old dream of discovering India and Eastern Christians had been fulfilled. The Thomas Christians on their part experienced a spontaneous joy at the arrival of powerful Christians from the West and desired Portuguese help to strengthen their privileged existence in India. When Vasco da Gama arrived at Cochin on his second voyage (1502), a delegation of Thomas Christians went to meet him and implored protection. The cordial relation thus established continued for two decades. However, when the Portuguese penetrated into the interiors of Kerala and into the churches of the St. Thomas Christians, they realized that these Christians were neither subject to Rome nor similar in church traditions. They found that these Christians were followers of the East Syrian Church, that Eastern bishops looked after them, and that the Patriarch in Babylon was considered their ecclesiastical head. Since the Pope had granted the Portuguese crown sovereign rights over eastern lands under their sway, the Portuguese thought that by right the Thomas Christians should be under their control, and they worked among the St. Thomas Christians for one and a half centuries to achieve this aim.
When the Portuguese came, the Church of St. Thomas was following the traditions of the East Syrian Church. There were about a dozen bishops from that Church among the St. Thomas Christians in the 16th century. From a letter of five East Syrian bishops to their Patriarch in Babylon (1504), it is known that there were in Malabar about thirty thousand families of St. Thomas Christians; new churches were being built, and they were prosperous and living in peace. Mar Jacob, the last among these East Syrian bishops, lived and led the Church of St. Thomas till his death in 1552. After his death the Roman Catholics intensified their efforts to subdue the Church of St. Thomas and to prevent any fresh arrivals of bishops from Babylon.
Immediately after the death of Bishop Mar Abraham, the St. Thomas Christians were forced to meet in the infamous Synod of Udayamperoor (1599), which declared that they were under Rome from then on. The major architects behind the convocation, deliberation, framing and execution of the synod's decrees were the Jesuits of the Vaipikotta Seminary. The convoker, presider, and judge was the Roman Catholic Archbishop Dom Alexios Menezis of Goa. The synod was held for eight days. The synodal decrees were aimed at the total transformation of the church of St. Thomas into Roman Catholic faith, polity and discipline. It decreed that the Supreme Head of the church of St. Thomas was the Pope of Rome; the Patriarch of Babylon was condemned as a heretic and contact with him declared perilous. The norms of the Council of Trent were enforced; priests were to be celibate by compulsion; the Malabar church was divided into parishes with a parish priest directly appointed by Portuguese authorities. All Syriac books were to be handed over for burning so that no memory of East Syrian connections remained.
Under the leadership of the Archdeacon, the Thomas Christians reacted by asking for the release of Ahatalla, who had been made captive by the Portuguese at Mylapore. When all appeals failed and news spread that he had been drowned by the Portuguese, tension mounted. At the Coonen Cross Oath on Friday, January 3, 1653, at Mattanchery near Kochi, the Thomas Christians declared that "till the end neither the Thomas Christians nor their generations would obey the church of Rome or the Portuguese or Jesuits, but only obey their Archdeacon Thomas." All historians agree that after the Oath practically the whole body of the Thomas Christians joined together against Roman Catholic supremacy. Archdeacon Thomas was later elevated to the status of bishop with the title Mar Thoma by the laying on of hands of twelve leading priests at Allangad on May 22, 1653, with the unanimous consent of the whole Church. Despite efforts by Rome and the Portuguese to regain control, about half of the people did not yield and maintained their Eastern character and ecclesiastical freedom—the tradition that continues today in the Malankara Orthodox Syrian Church.