The party that sought to preserve the Church's freedom appealed to several Eastern Christian Centers for help in restoring its Episcopal succession. The Antiochian Syrian Patriarch responded and sent to India a Bishop, Metropolitan Mar Gregorios of Jerusalem who came to India in 1665. The Archdeacon who had been declared in the meantime to be Metropolitan Mar Thoma I by the laying on of hands by twelve Presbyters was now confirmed by him in his Episcopal rank, and both of them worked together to organize the church on firm footing. Thus began the formal relationship with the Syrian Orthodox Church, as it happened, in explicit support of the traditional autonomy of the Indian Church. Mar Thoma I was followed in succession by a series of Prelates with the same name till 1816 when the last of them namely Mar Thoma IX came to the scene, but was soon replaced by Mar Dionysius II.

 Malankara Orthodox Church had felt the need of assistance for establishing systematic education for its clergy, teaching the people in the faith, instructing the clergy in properly celebrating the liturgical services and above all assistance in the maintenance of the Episcopal succession intact. But the Orthodox Church maintained its autonomous administration and life under local leadership. Even the help from the Antiochian Syrian Patriarch was without any idea of formally submitting to his jurisdiction, but only for an over all spiritual supervision and of keeping to a friendly relation.

 There were differences of opinion over the authority of the Patriarch in the Malankara Church and it created certain difficulties. But the Church has always been successful in maintaining its freedom and never allowed any foreign domination.