For a comprehensive understanding of this article, first read:
Apostle Thomas in India
Early Christians of India
Western Influence on Thomas Christians
The Latinising policy of the Portuguese in Malabar in the 17th century found no bound, and continued with some cruel deeds which so infuriated the Malabar Christians. Roz S.J., who was appointed as successor to Mar Abraham was a Latiniser. The Mass, the Ritual Portions of the Divine Office were all Latinised by him. The ancient Ritual was substituted by a translation of the Roman one with the peculiarities of the diocese of Braga, Portugal. In 1608 the archdeacon sent his complaints to the Papal Nuncio in Lisbon, but got no reply. The archdeacon was even excommunicated, though absolved in 1615. Quarrels again broke out in 1618, since (it is said) the archdeacon was not made Administrator when Roz S.J. went to Goa. Roz S.J. even had recourse to arms in order to curb the activities of the archdeacon.
Since 1641, a regular fight ensued between the new archbishop Garcia S.J. and the new archdeacon Thomas. The archdeacon boasted that the archbishop could not do anything without his consent. Garcia S.J. had to yield to the archdeacon in many things, and it is said that the archdeacon had secret correspondence with the Nestorian, Coptic and other Patriarchs. But according to some he wrote only to the (Catholic) East Syrian (Chaldean) Patriarch.
In 1652 there arrived at Mylapore one Ahatallah who claimed to be the "Patriarch of All India and China, sent by the Pope". (It seems now an established fact that Ahatallah originally hailed from the Jacobite Church of Syria. Later he was converted to Catholicism. He came to India at the request of the Coptic patriarch while he was staying in Cairo. He seems to have remained faithful in the Catholic allegiance till his death). The whole Christian community was roused, and insurrections took place everywhere. Fr. Manoel de Leira S.J. from Mylapore gave secret information to the Portuguese authorities about the movements of Ahatallah. The Portuguese authorities without delay deported him to Goa via Cochin.
The archdeacon reached Cochin with a number of soldiers and demanded to see the "Patriarch" (Ahatallah) and to examine his credentials. He said he would not demand the Patriarch's release if the credentials were found false. The Portuguese agreed first, but soon they deported Ahatallah to Goa without showing him or his credentials to the archdeacon and to his followers. The behavior of archbishop Gracia S.J. is said to have been haughty. The Portuguese contention was that no bishop could legitimately come to the Thomas Christians without the knowledge of the Portuguese crown. They thought that Ahatallah was a 'Nestorian' or an East-Syrian intruder.
A false rumour was spread that Ahatallah was drowned by the Portuguese off the coast of Cochin. Then the archdeacon wrote to the Portuguese captain saying: "Moreover, Captain, we beg your honor that, for the love of God and the service of the Christian Community, you work hard to bring back the Patriarch". But it produced no result. Next, all who were present moved to Mattancherry near Cochin, tied a long rope, as tradition says, to the open air cross called the Coonan Cross, and holding the rope, swore they would never be under the Paulists (i.e. the Jesuits). This took place on 3rd January, 1653.
The rift caused in the community by the forced removal of Ahatallah from India, is to be understood in the light of the attachment the Indian Christians still cherished for the East-Syrian Church. The fact that the Thomas Christians always remained very attached to the bishops of their own Rite and merely tolerated the government of the Latin bishops, is clear from the many petitions they sent to many authorities. The dream of the Christians, aroused by the arrival of Ahatallah, to be once more an autonomous Church under a Syrian prelate was shattered. The oath and the tragic events that followed were expressions of their bitter disappointment. The "Coonan Cross" Oath, marked the final outbreak of the storm that had been gathering on the horizon for a century.
The malcontents held a meeting at Edapally and then met at Alangat on May 22, 1653, swore on the Gospel that they would not obey Garcia S.J. Twelve priests imposed their hands on archdeacon Thomas calling him archbishop Mar Thomas I. The assembled were made to believe that they were empowered to this by the order of Ahatallah whose letter (a falsification) was also read aloud. The pseudo-archbishop was given four councilors. One may ask here whether it was a real consecration or a mere installation that the twelve priests had intended in imposing their hands on the archdeacon. Any how, the archdeacon began to exercise powers of Episcopal order though he openly tried to obtain valid Episcopal consecration.
Italian Carmelites were sent to Malabar by Pope Alexander VII to reconcile the malcontents. Then the Pope appointed Fr. Sebastiani O.C.D. as Apostolic Administrator of Cranganore in 1659, and he was helped by an Indian priest, Chandy Parambil. In 1663 when Sebastiani had to leave India, Fr. Chandy Parambil (Alexander de Campo) was made the first Vicar Apostolic of Malabar under the Propaganda Jurisdiction. After the demise of Mar Alexander, no indigenous Syrian bishop was appointed to succeed him. The attempt of reconciliation was successful to a certain extent, and many including three councilors of the pseudo-archbishop, came back to the Catholic fold. However, the archdeacon (Mar Thomas I) and many of his followers were not happy to come back.
In the year 1665 the Jacobite bishop Mar Gregorios of Jerusalem, arrived in Kerala. He infiltrated anti-Roman ideas and introduced Jacobatism (Monophysitism) among the followers of the pseudo-archbishop Thomas I to bring them under the Jacobite patriarch of Antioch. Their good faith was already shaken at the solemn excommunication served to the pseudo-archbishop by Sebastiani. This is how the revolt of 1653 turned out into a schism. It split the community vertically into two groups, one in communion with Rome and the other establishing a new allegiance, namely to the Jacobite Church of Antioch. Because of this new allegiance, the malcontents began to be called "Puthenkuttukar" (people of new allegiance).
The community under Thomas I began cultivating relations with Jacobite patriarch of Antioch. Ever since that time Jacobite bishops were sent to India from time to time by the patriarch. Thomas I was succeeded by Thomas II, Thomas III and so on until Thomas VI who succeeded Thomas V in 1765. At that time there were two Jacobite bishops in Kerala who became rivals. Ramban (an ecclesiastical dignitary) Kattumangatt assumed the name Cyril (Kurillos) and separated himself from the communion of Thomas VI. He headed a community at Thozhiyur or Anjoor in north, in British Malabar. This community came to be known as the "Independent Jacobite Church of Malabar". It was because of pressure, a second one had to be consecrated as Mar Thomas VI. After consecration he assumed the name Dionysius I. He attempted to go back to Catholicism, but when his demand to be recognized as a bishop was rejected by the Catholic authorities, he returned to Jacobitism. For more details, see The Syro-Malankara Church.
Split over Patriarchal Authority
In 1909 Mar Ignatius Abdalla Satuff, Jacobite Patriarch of Antioch, visited Kerala and got involved in a conflict with Mar Dionysius VI, the Jacobite metropolitan of India. While patriarch insisted on comprehensive jurisdiction over the Malabar Church, Dionysius would allow him only the spiritual power - the right to consecrate bishops and chrism (holy oil) for the Church. This conflict split the Church again into two: Dionysius and party against the patriarch (Methran Kakshi, ie., Bishop's Party), and the second group under Cyril, another Malabar Jacobite bishop, for the patriarch (Bava Kakshi, ie., Patriarch's Party). The Bishops Party appealed to Abdul Masih, a deposed patriarch of Antioch. He came to Kerala and installed Dionysius as the "Catholicos of Malabar". The Methran Kakshi calls itself the "Syrian Orthodox Church of India". The Bava Kakshi calls itself the "Jacobite Syrian Orthodox Church (of India)".
In 1861, the arrival of a Chaldean Catholic bishop, Thomas Rokkos sent by the Chaldean patriarch created more problems among Catholics of the Thomas Christians. He was excommunicated on his arrival by the Vicar apostolic of Varapuzha, and a schism followed. Another Chaldean bishop, Elias Melus arrived in 1874 and he too met with the same fate. The followers of the schism Melus created are popularly known as the Surais who owe allegiance to the Syrian Nestorian patriarch. They are seen in and around Thrissur in Kerala.
Approximate number of the members of these Churches
Syrian Orthodox Church (Methran Kakshi) - 1,100,000
Jacobite Syrian Orthodox (Bava Kakshi) - 1,000,000
Independent Jacobites (Thozhiyur) - 9,000
Church of the East (Nestorians/Surais) - 100,000