1635: Off to America: As has been noted, Thomas and Alice Welles probably became strong Puritans in the late 1620s as they abruptly changed the naming patterns of their children. Welles' neighbors, George Wyllys, the Griswolds, Rev. Ephraim Huit and Daniel Clark were all becoming associated with each other, with Say and Sele, and with the group around Hooker in and around Braintree. Brook and Say and Sele were making plans to develop the area now known as Connecticut. The religious motivation and the economic opportunities coalesced in the minds and hearts of Thomas and Alice Welles. Although economic considerations would have been important, scholars agree that the religious motivation was paramount, especially in the early years of the Great Migration. People of comfortable means and social standing such as the Welles family usually do not leave a secure living and bring their young children across perils and into perils merely for material gain, but because they are motivated by a very strong conviction that they are doing right and that their activities will be guided and blessed by God. Virtually all the five thousand families who came to New England in the Great Migration had an individual experience with God which they felt enabled them to undertake this great uprooting and transplanting into an entirely new and untried wilderness to fulfill a divine purpose for themselves and their nation. They endured the insecurities and discomforts out on an individual inner conviction that they were pursuing God's will and would be blessed in and through that undertaking. Though no writings survive to tell us of the feelings of Thomas Welles, such thoughts were expressed many times over in the journals of those who kept them, and were a given part of the mindset of the first settlers in southern New England. Welles' close association with Hooker and the high regard in which he was held from the initial days of the colony underscore the degree to which he was held to be a man of faith in a community where faith was a cherished virtue. While he may have been considering his personal motivations for removal to New England, Fiennes may have been recognizing that Welles' leadership and secretarial skills would be useful in administering the new venture. It has been suggested that although Welles may not have been actually employed as Say and Sele's secretary, the nobleman may have used this notion as a ploy to disguise to other authorities Welles' more religious reasons for removal.

When Thomas and Alice prepared to emigrate to New England, they disposed of the Burmington property over to James Fiennes, and William Sprigg. This action took place 20 Aug 1635. Court testimony shows that Thomas, Alice, and their six children took ship to the new world soon after.

At least one other Thomas Welles came to Boston in 1635. This second man we now know as Thomas Welles of Ipswich. He is probably the Thomas who came on the "Susan and Ellen." If Thomas of Ipswich went immediately to Ipswich upon his arrival, then the Thomas Welles listed as a householder in Cambridge on 8 Feb 1635/6 is the one who later moved with other residents of Cambridge to Hartford, CT. By 9 Jun 1636, Thomas and Alice were in the Boston area. On that day, they testified in front of John Winthrop and Thomas Dudley pertaining to the deed of the Burmington properly.

No evidence exists that Welles was ever at Saybrook Colony. To have been part of the community at Saybrook Colony, given his presence in Hartford in the winter of 1637 and his presence in Cambridge in Feb 1636, he would have to have been there in the winter months of 1636. At that time Saybrook was only a fort manned by soldiers. The first family there was that of Gov. George Fenwick and his wife a few years later. The most logical conclusion is that Welles joined Hooker, whom he knew either personally or by reputation in England, at Cambridge in 1635, stayed about a year, entering the list of householders, and that he and his family were part of the company of one hundred who trekked to Connecticut in June 1636, journeying over existing Indian trails from the Bay to the River for a period of about ten days to two weeks. The trail had been developed by the Indians to provide passage between the Bay and the Falls about a hundred miles west where the shad spawned their young every spring, and fish could easily be caught and dried. The trail followed the most level terrain and crossed the least number of streams. Parts of the Old Connecticut Path still exists, unpaved, in Ashford and along Lake Shenipsit in Ellington.

Governing Philosophy: Welles' administrative and clerical skills must have been well-known to the community as he was chosen as a magistrate and as clerk of the General Court at its first meeting in Mar 1637. That court was the first that met independent of the authority of Massachusetts. In the opening session of their independent General Court, the three river towns were given their current names of Windsor, Hartford, and Wethersfield. That court declared war on the Pequots to avenge the savage murders of several early settlers. In the following year, Rev. Thomas Hooker preached his famous sermon in which he declared that "the foundation of authority is laid in the free consent of the people." He closed his sermon with the challenge, "As God has given us liberty, let us take it" (Register and Manual, State of Connecticut, Hartford, 1984, p. 55). In his years as a pastor in England and in the Massachusetts Bay Colony, he had developed a political philosopy shared by Roger Ludlow and Rev. John Warham, which led to the removal of those parties from the Massachusetts Bay to the Connecticut River. While agreeing on theology, Warham and Hooker differed with Gay. John Winthrop and Rev. John Cotton on the nature of government. Winthrop and Cotton believed that God spoke only through the religious officials. Warham and Hooker believed that God spoke to all believers and that the entire body could therefore make political decisions. Hooker based his theology on the Old Testament incident in which God told Moses to take ten leaders elected by each of the twelve tribes of Israel to help him to render judgments. The General Court, including Welles, spent the ensuing year working this theory into a political document under the guidance of attorney Roger Ludlow, an organizer of the Warham party under Rev. John White of Dorchester in Dorset. The result was the Fundamental Orders of Connecticut. This document was the world's first written Constitution, for the first time placing basing of the authority of the government on the people. It claimed that the basis of government authority lies in the people themselves, not a king or any other source, and that the people have the right to chose their own leaders. The little colony along the river, consisting of perhaps five hundred individuals, had declared itself an independent political entity concerning internal affairs, while owing general allegiance to the British crown.

Government Service in Connecticut: Thomas Welles served for many years on the General Court which was the ruling body of the Connecticut Colony. During the first three years of his attendance, 1637-1639, the Court had two representatives from each of the three towns that then comprised the colony. These men met without titles or moderators. A new structure was set for the General Court by the Fundamental Orders of 1639. The General Court consisted of a council of Magistrates and one of Deputies. This Court met twice a year for Spring and Fall sessions.

The Deputies and Magistrates were chosen by the towns whereas the Governor and Deputy Governor were elected by the General Court itself. The Deputies were chosen twice a year in town meetings in the Connecticut Colony. Each town would pick three or four men to represent it in the General Court. Each town also chose one or two Magistrates. What made the election of Magistrates different from that of Deputies was that Magistrates could only be chosen from a list that the General Court had prepared for the town at the previous session. Thus, each man elected a Magistrate had previous experience in the General Court. Appendix B provides a list of the sessions Thomas attended and the positions within the Court to which he was elected.

In the 1639 session Welles was elected Treasurer of the Colony. Two years later, after his election as Secretary in 1641, he transcribed the Fundamental Orders into the official record book in his own hand. To guard against authority becoming concentrated in one individual, the General Court limited the terms of governors to one year at at time, though a man could serve as governor more than once. For nearly all of the remaining twenty years of his life Welles attended the sessions of the General Court, which both made laws and, sitting as the Particular Court, tried cases under the law. He rotated among the major offices of treasurer, secretary, deputy governor, and governor. He was elected governor in his own right in 1655 and 1658. As noted, he served on the committee to negotiate the merger with Saybrook Colony. He also served as Commissioner from Connecticut to the meeting of the United Colonies of Connecticut, New Haven, Plymouth, and Massachusetts Bay in 1649, 1654, and 1659. As magistrate, he sat on the judge's panel for Connecticut's earliest witchcraft trials in 1648, 1651 and 1654. He heard the cases concerning Mary Johnson, John and Joan Carrington, and Lydia Gilbert. He is not noted to have had any special role in these proceedings. The trials are well-documented in The Public Records of the Connecticut Colony, Records of the Particular Court of Connecticut 1639-1663, and Richard G. Tomlinson's Witchcraft Trials of Connecticut. Thomas also served on the War Commission for Wethersfield in1653.

He became involved in the establishment of the settlement at Stratford, named for the town near his home village in England. His son John was sent to oversee his interests there. According to tradition, the last child of Thomas and Alice, a son named Joseph, was born shortly after their arrival in Connecticut. Primary documentary evidence for this son has not yet surfaced. He apparently did not survive as he is not mentioned in his father's will. However, he lived long enough to have his memory perpetuated in the name of some of his sibling's descendants. A few years later Alice died, not having reached the age of fifty. in 1646 Thomas married Elizabeth Foote, widow of Nathaniel Foote who died in Wethersfield in 1643, and sister of Joseph Deming of Wethersfield. She was unwilling to leave the homestead of many acres she was managing after her husband's death. As a result, one of the highest officers in the colony left his home in the center of Hartford and moved to Wethersfield with his younger children, Samuel and Sarah who were raised her younger children Frances, Sarah, and Rebecca.

Thomas wrote his will on 7 Nov 1659. He seemed to be in good health on the evening of 14 Jan 1659/60, being well after supper, but dead by midnight. His will left his wife the use of half his housing and orchard, with her own land to his return to her. His own land and house went to his grandson Robert, the only child of his oldest son to live in Wethersfield. He left land to sons Samuel and Thomas, and to Thomas son of the deceased son John, 20 pounds to Thomas, Samuel, Mary's children, Anne, Sarah, and 10 pounds to Mary Robbins' children. Elizabeth lived another 22 years, leaving her estate to her children and grandchildren by Nathaniel Foote.