A crisis followed the Coonan Cross Oath. The rejection of the Latin rule by the St. Thomas Christians was so thorough that it demanded Rome’s intervention. The Propaganda Congregation of Rome acted promptly and dispatched Carmelite monks to India. One of them, Joseph Sebastiani OCD, was made the bishop and vicar apostolic of Malabar in 1661. Meanwhile the Dutch who were in competition with the Portuguese, captured Cochin and asked Sebastiani to leave India. Chandy Parambil, a son of the soil, was consecrated bishop and appointed vicar apostolic in Sebastiani’s place. After Chandy’s death in 1687, there was a period of confusion.

As a result of an agreement between Rome and the Dutch, the Holy See, could appoint an Italian Carmelite as the vicar apostolic of Malabar in 1770. The Carmelite vicar apostolic eventually took residence at Varapuzha. These vicars apostolic were under the Propaganda Congregation of Rome. There were also archbishops or administrators appointed by the Portuguese Padroado who resided at Kodungallur. Thus the Kerala Christians were under two jurisdictions: the Propaganda represented by the vicar apostolic who resided at Varapuzha and the Padroado represented by the Archbishop of Kodungallur.

In the course of time, the grievance of St. Thomas Christians against the foreign missionaries gained momentum. Many conventions (pothuyogams) were held at Angamaly to orchestrate their grievances, of which the one in 1778 decided to send a delegation to Rome. A few years after this convention, Fr. Joseph Kariattil and Fr. Thomas Paremmakkal made their historic journey to Rome and Lisbon. In 1782, Kariattil was consecrated Archbishop of Kodungallur in Lisbon, but on his way back before he could reach Kerala, he died in Goa in 1786. Thomas Paremmakkal kept a journal of their journey. This journal is the famous Varthamanapusthakam. Following the death of his companion, Paremmakkal was made the administrator (Govarnador) of Kodungallur.

This was the time of great turmoil. The agitation against foreign vicars apostolic continued to gain momentum. In 1787, representatives of 84 churches assembled at Angamaly and drew up a document known as the Ang amaly Podiola, which lists the sins of commission and omission of the foreign missionaries. Rome took these developments seriously and sent delegates to study the situation.

In the light of the report the delegates submitted, Pope Leo XIII decreed in 1887 the separation of the Rite of the St. Thomas Catholics from that of the Latins. The Pope erected two vicariates apostolic (quasi-dioceses) for the St. Thomas Catholics: Trichur and Kottayam, but appointed two Latin bishops, Bishop Adolf Medlycot, an Anglo-Indian and Bishop Charles Levinge, a French Jesuit, as their vicars apostolic. The plea for native bishops continued: In 1896, the Pope decreed the erection of three vicariates for the St. Thomas Catholics: Thrichur, Ernakulam and Changanacherry. This time the vicariates were entrusted to the care of native Indian bishops: John Menachery, Louis Pazheparambil and Mathew Makil respectively.

In 1911, Pius X erected a fourth vicariate, the vicariate of Kottayam for the southists, an endogamous community (a community which allows marriage only within itself) among the St. Thomas Christians. They claim to be the descendants of the East-Syrian Christians who migrated from Persia along with Knai Thomman. The descendants of the original community of St. Thomas Christians are known as the Northists. On December 2, 1923 Pope Pius XI established the Syro Malabar Hierarchy in India with Ernakulam as the Metropolitan See and Changanacherry, Thrissur and Kottayam as suffagrans.

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