Thomas was the second son of Abraham Malpan born in 1837, the year in which the reformation began. Abraham Malpan's four older children were daughters. When the youngest daughter was born, a learned Brahmin friend of Malpan visited the house to see the newly born. Malpan's wife Aleyamma was reluctant to have the baby seen, as she felt ashamed to show a female offspring, the fourth in a row, to the distinguished visitor. The wise Brahmin understood Aleyamma's reluctance and told her, "Don't be disheartened. You will now have four sons and they will be princes". His prophecy came true as two of her sons, Thomas and Titus (who was the youngest) became Metropolitans and princes of the Church and the other two, Mathai and Kochukoshy, eminent members of the society.

Thomas grew up as a happy child with his siblings enjoying the beautiful Pampa River almost at the doorstep, and the vast riverbed as their playground. He was six years of age when his cousin, Mathews Mar Athanasius, returned from Mardin as the Metropolitan of the Malankara Syrian Church. But when he was 9, tragedy struck the family. His father, Abraham Malpan, suddenly passed away at the early age of 50. Metropolitan Mathews became the head of the family and took charge of his cousins, their welfare and education. Thomas had his primary education at Maramon and thereafter the Metropolitan took him to Kottayam to study at the C.M.S. English School and the Seminary. Thomas had the company of Metropolitan's sister's son, Cherukara Philipose, who later became Malpan and leader of reformation. They both studied Malayalam, Sanskrit, Syriac, English and Church's canons and rituals. They were both ordained deacons. Meanwhile Thomas's younger brother, Titus, joined them at Kottayam and pursued similar subjects. The studies at the Seminary and at the English School were better than at later times, as there were only a few students who received good personal attention from the teachers. The study of languages was given priority but other subjects like Mathematics, Geography and History were also taught. Most of the students were boarders and as such they had good campus life and sharing of ideas. Some of the students like Philipose Malpan of the Syrian Church and Archdeacon Oommen Mammen of the Anglican Church became leading clergymen.

After their studies at Kottayam, the Metropolitan decided to send Thomas and Titus to Madras for further studies. Thomas had by then been ordained Kasissa and Titus had been ordained Deacon. The journey to Madras was not easy, as the train was available only for part of the journey. In Madras they had to stay in a rented house, as there were no student hostels. oth of them excelled in studies and Thomas got a medal for his proficiency in Mathematics. Madras city was beginning to grow and had all the problems of growing city, including poor hygiene, in the nineteenth century. It affected their health and they were forced to return to Maramon after 2 years. However, the stay in Madras helped them immensely as they continued their studies of languages including Tamil and got acquainted with church leaders, English and Indian, from different denominations in Madras.

Thomas Kasissa returned from Madras in 1862 and he worked for a while as parish priest in Maramon. He did not have the good fortune to learn about reformation from his father but he was in touch with Malpan's colleagues. Further, thanks to his proficiency in languages he was ale to read ancient books in Syriac and the contemporary books in Malayalam, English and Tamil. He was able to preach effectively and instruct the congregation in the Bible and reformation theology. He had an impressive personality, being tall and well built in physique as well as gregarious and friendly in his approach to people.

Before long the Metropolitan appointed Thomas Kathanar as his chaplain and secretary and Thomas moved his residence to Kottayam. The workload of the Metropolitan was increasing steadily and it was clear to all church leaders that he needed the assistance of a Saffragan Bishop. A number of them including Kurien Writer of Kunnumpurath family in Kottayam, who was a prominent member of the Church, urged the Metropolitan to consecrate Thomas Kathanar as they were all convinced that he was a worthy successor. The Metropolitan tarried for a while, but gave in finally in view of the assistance of Metropolitan Kurilose of Thozhiyur, on 1st June 1868. The young Bishop stayed on in the Seminary. He was given the responsibility of expanding the teaching at the Seminary, which he was able to do with the cooperation of Cherukara Philipose, who was the chief Malpan at the Seminary. After a while Bishop Thomas handed over the responsibility to Philipose Malpan to be able to give adequate attention to duties of Church administration as Suffragan Metropolitan.

Bishop Thomas was Suffragan for nine years and Metropolitan for 16 years. The position of the Saffragan Metropolitan was unusual in the Malankara Church till then, as the tradition of the Church was to have only one Bishop, the Metropolitan. This was because of the fact that Church was small and the Metropolitan could manage the administration by himself. The Metropolitan spent most of the time visiting the parishes in Travancore and Cochin and he issued Episcopal circulars from whichever parish he was visiting. An entourage of chaplain, secretaries, bodyguards and other servants traveled with him and those who wished to see him visited him at whichever parish he happened to be camping.

Metropolitan Mathews decided to make certain changes in this respect. He continued to visit parishes and he also took upon himself to liaises with the government on behalf of his people by maintaining good rapport with the Dewans and Maharajahs of Travancore and Cochin. The Suffragan shared the parish visits with the Metropolitan and maintained the Episcopal office in the Seminary. Whenever he visited the parishes, the Suffragan conducted the Services according to the reformed liturgy. He was a good revivalist speaker and he gave the ministry of the Word due importance in the Holy Communion Service. The Suffragan was a close adviser to the Metropolitan who, though inclined to e somewhat autocratic, still sought and accepted the advice of the Suffragan. While at Kottayam, they both stayed at the Seminary. The facilitated mutual consultation, was affording useful experience to the Suffragan.

Metropolitan Mathews Mar Athanasios died on 15 July 1877. The Suffragan was the acknowledged successor and he assumed the office of the Metropolitan and the steward of Church property along with the Trustees. Two months after the death of Metropolitan Mathews a memorial dinner [Adiantharam] was held, as per custom, at the Seminary under the leadership of Metropolitan Thomas with the assistance of leading clergy like Thazhath Chandapilla Kathanar [Thazhath Achen], Philipose Malpan and Kovoor Iype Thoma Kathanar. There were about eight thousand particpants representing all the parishes in Travancore and Cochin.

He was a meticulous correspondent both in Malayalam and English. Although he had no means to keep copies of his letters, he kept a careful note of the letters he had written to each parish and individuals, both clergy and laity, and insisted on replies from his correspondents. When the Church had important visitors, like the Governor of Madras, Anglican Bishops, or Thozhiyur Metropolitans, he instructed the parishes in detail on protocols how to receive and welcome them. He wrote letters to various Hindu and Muslim friends, arranged to meet them and enquired of the welfare of their families. His compassion and concerns extended to all people, and was not confined to his supporters. He had no hesitation, like his predecessor, in approaching senior government. During a visit by Maharajah, Visakham thirunal, to Kottayam in 1880 the Mar Thoma Church gave him a reception and His Highness said, " If Parasuraman visits Kerala he will not find a community better in loyalty and patriotism than the Syrian Christians". These were plaudits for all Syrian Christians.

The Metropolitan Thomas Mar Athanasios kept in touch by letters with English missionaries, the Anglican Bishops of Madras and Calcutta, the Governor of Madras and senior British officials. When they visited any area in Kerala, they were invited to visit the local Mar Thoma church. When he met these dignitaries he took with him a delegation of senior clergy and laity.

In 1888, 12 Church leaders, two clergy and ten laity, met at residence of Kadavil Achen in Kallisseri, near Chengannoor. They came together for prayer meeting. They decided to form an Association called Malankara Mar Thoma Evangelistic Association. Metropolitan Thomas gave blessings to this association. A Church Magazine under the name of 'The Malankara Sabha Tharaka' was started in which name it known to this day.

In his letter of 1882 to Kuriannur parish he appealed to the womenfolk to emulate the women mentioned in Exodus Chapter 35 and to donate a handful of uncooked rice daily and give it to Church. This was known as Pidiyari. To enable them to form the habit he distributed to every housewife earthenware pots from the nearby village Poovathur, famous for earthenware pottery. The pots were collected at regular intervals and the contents auctioned. Secondly, he asked the farmers to give a coconut from every coconut tree they owned, a bunch of areca nuts and bunch of banana. Those who cultivated paddy were asked to make an allocation from their harvest for the Church. The traders had to give one Chakram per boat per month; as well trade was river-borne. In addition, farmers and traders were to make voluntary contribution from the farm produce and trading income. He also instructed that the administration of the finance, for the Kuriannur church had to be handled by a treasurer, Punnathundil Varghese, and assisted by Thatchilethu Kochukunju, an accountant. He suggested building a treasure chest with three locks, the keys of which were to be kept to be kept by the vicar, the treasurer and the accountant. This way he evolved for each parish a systematic method to garner church finance and provided a detailed financial plan. It was a heavy burden to raise the necessary finance even to support the simple life of the Metropolitan and the clergy.

Later Metropolitan started living at the ancestral Maramon Parish. The parish built an annexe to the church and that became the Episcopal residence for his life-time. Maramon Church being on the banks of the river Pampa, he could travel by boat to several parishes easily. He contributed to the economic development of the area by helping to organize a market in Kozhenchery, which is still flourishing. There the farmers could bring their produce and sell to the traders who transported their goods to distant townships by boat. He wanted to start English schools in Kozhencherry and Maramon which did not happen during his life-time.

In November 1892 the Governor of Madras visited Travancore and he wanted to meet metropolitan Thomas as they were in correspondence. Metropolitan requested Thazhathu Achen, the pillar of the Church in the Kottayam area, to organize a reception at Kottayam Cheriyapally. The Governor was received at Pallam and escorted by a festooned boat to Kodimatha and thereafter by land to Cheriapally to meet the Metropolitan.

Metropolitan's life was one of the ceaseless work and stress, both physical and mental. He had been suffering from rheumatism from an early age and by the age of 50 his health began to fail. He was under regular treatment of expert Ayurveda physicians. In July 1893, there was an aggravation of his rheumatism and the physicians prescribed an elaborate system of treatment which was not possible in his frugal residence at the Maramon church annexe. So he moved by boat to the ancestral house at Palakunnathu which was spacious and on the riverbank about a mile away. He had the feeling that his life was approaching its end. So he visited the houses of his two brothers which were also on the river bank on the way.

While undergoing treatment at Palakunnathu house he grew weaker. The news spread and there was a regular stream of anxious visitors, clergy and laity. He did not have the strength to talk to them. He had a stream of distinguished visitors including Jacobite Metropolitans Pulikkottil Mar Dionysius, accompanied by Vattasseril Geevargehese Malpan (Later Jacobite Metropolitan).

Within days, Metropolitan Thomas breathed his last and the whole Mar Thoma Church was shaken to its foundations and overwhelmed with grief for the loss of the brave Metropolitan who led them courageously through unimaginable difficulties and brought them to stability. Their sorrow was greater as they were left without a successor and the Church felt literally orphaned. The brave clergy and laity rallied under the leadership of the indomitable Vicar General Kovoor Achen. The Thozhiyur Metropolitan could not come due to floods, being the height of the monsoon. So Kovoor Achen gave the lead in the funeral service at the Maramon Church and during the Service Kottureth Achen said a tearful prayer, "Lord when Moses died you had provided a Joshua to lead the people but now we have nobody." and then he broke down with overwhelming emotion and could not continue. Kovoor Achen, standing next to him who was himself in tears, stepped in to complete the prayer by saying, "Lord of Isrel and God of fathers, please provide us a leader." The Metropolitan was buried with due Episcopal honours on the precincts of the Maramon church alongside the tombs of Metropoitan Mathews Mar Athanasios and Abraham Malpan.