From the hypothesized arrival of St. Thomas in A.D. 52 till the Koonan Cross in 1653 the history of the Indian church is common. Not much is known about the early history of the St. Thomas Christians, but two facts stand out clearly. Between the 3rd and the 9th centuries there were waves of immigrants from Mesopotamia (corresponds to regions of modern Iraq, Syria, Turkey and Iran) to Kerala, and from the early centuries, this Church, with its liturgical center in Edessa, Mesopotamia, had also claimed its origin from St. Thomas. Thus the East Syrian or Chaldean liturgy was used in Kerala until the 17th century. The Syrian Church (using the Syriac liturgy) in Kerala was undivided until the advent of the Portuguese.

The Koonan Cross Oath (Koonan Kurishu Sathyam) was taken by a group of Saint Thomas Christians, reacting to the persecution of their Church by the Portuguese colonials and Jesuit missionaries who sought to bring it under Portuguese Padroado or Propaganda Fide. St. Thomas Christians remained in communion with the Church of the East until their encounter with the Portuguese in 1498. The Portuguese refused to accept the legitimate authority of the Indian hierarchy and its relation with the East Syrians.

In accordance with the request of the Syrian Christians of Kerala, the Patriarch of Babylon sent a Syrian priest to Kerala but soon news spread that this priest was caught and executed by the Portuguese. Enraged at this, thousands of Syrian Christians assembled near the historic church at Mattancherry near Fort Kochi, and touching at the old cross there (a bend one) they took a pledge that in future they would not obey the Arch Bishop. Those who swore the oath vowed that neither they or their descendants to come would have anything to do with the Portuguese Padroado and that they would stop obeying the Jesuit missionaries. After the Oath twelve priests laid hands on the head of the archdeacon, who was connected to the leaning cross by a rope, and ordained him Bishop. The several thousand other people who were there also took hold of the rope to signify their participation in the Oath. This marked a turning point in the history of the Syrian Christian church of Kerala. The rift in the Christian church in Kerala became a reality.

The families/households represented by all these people and others later accepted the Antiochean tradition. They now form the Malankara Syrian Orthodox Church (or the autocephalous Indian Orthodox Church), the Mar Thoma Church, and the Jacobite Church. The group of Saint Thomas Christians who did not participate in the Coonan Cross, remained with Portuguese Padroado later came under papal authority and are called the Syro-Malabar Church.

Ref:

1. Cross-reference of the account by Fr. Dr.Geevarghese Panicker, a priest of the Syro-Malanakara Church which accepted the Pope on 20 September 1930, published in the Journal Of St. Thomas Christians, Vol II, No.2., Oct-Dec 2000.
2. NCERT, Std X, Chapter 8, Medieval Kerala.
3. Wikipedia article on Coonan Cross