The Portuguese then tried to bring the Indian Orthodox Church under the roman papacy and to Latinize its rituals.
The Indian Christians vehemently opposed this,the Portuguese retaliated by burning our churches,destroying ancient manuscripts and documents,and imprisoning our leaders and priests.
They treated our priests and bishops with utmost disrespect and they are said to have insulted them by pulling at their beards and making fun of them..
They killed our priests and bishops.
"The Portuguese not only persecuted and killed all the bishops as they came from Antioch but their metran .... ..... And those Syrians who opposed his designs were persecuted and put to death." ("The Syrian Christians of Malabar" p.23
---texts of H. H. Meyers, Benjamin George Wilkinson, Ph. D
"The first Syrian prelate who was brought into antagonism with Rome, expiated his want of courage in the dungeons of the Inquisition. The second shared the same fate. A third whose sufferings are more worthy of consideration, died after much trial and tribulation in his diocese, denying the Pope's supremacy till the last." ("Christianity in India" p.24 by Kayes)
In 1653,a syriac bishop who was coming to India at the invitation of the Indian Orthodox Church was captured by the Portuguese and was murdered in cold blood under orders from Archbishop Menezes of Goa.
(Goa was the base of the portuguese colonialists in india)
This was too much,and a boiling point of anger against Rome had reached.
The enraged St.Thomas christians assembled by the thousands at a place called Mattancherry and gathered round a cross there.
They took an oath that day--"We or our descendants to come in the ages,will have nothing to do with the Church of Rome or its Pope"
This Oath is now famously known as the "Coonan Cross Oath".
They resolved to preserve the faith and autonomy of their Church and to elect its head. Accordingly, Archdeacon Thomas was raised to the title of Mar Thoma, the first in the long line up to Mar Thoma IX till 1816.
At the request of the Thomas Christians, the bishop, Mar Gregorios of Jerusalem came to India in 1664, confirmed the episcopal consecration of Mar Thoma I as the head of the Orthodox Church in India. The Antiochan Patriarch had come forward to help the Indian church in its moment of need.
This was a new age for the Indian Orthodox Church,it now had renewed contacts with other christian churches.
And by the blessings of St.Thomas,the Portuguese were soon ousted from India by the Dutch..the Dutch were a far more civilised and cultured people and even tried to help the Indian church in many ways,.though they were a protestant people.
Today,as a reminder of the Portuguese persecutions,there are two small eastern catholic rites(syro-malabar & syro-malankara) in india who left from our Mother Church.There are also some latin catholics on the coastal regions.