Despite the uncertainty of disputed land claims and the chaos of war, the residents of Bethel hung on. Bethel continued under the care of William Tennent, except for a period from June 1756 to September 1757 when Brainerd was again directed to serve as missionary to the group. In 1758 and 1759, Brainerd also served as chaplain to the Jersey Blues at the regimental post of Crown Point, New York.

Part of the continuity of Indian habitation of central New Jersey, and illustrative of the intricate relationship of inter-racial diplomacy that touched Bethel, was the story of Weequehela, a prominent sachem with ties to the colonial government of New Jersey. In 1709 the government had sought his support for raising Indian warriors in the ongoing conflict between British America and French Canada. In 1727, frustrated at the theft of his property by Captain John Leonard of South River Bridge (present-day Old Bridge village of East Brunswick), Weequehela killed Leonard. He was arrested at his plantation at what is now Spotswood, tried in Perth Amboy and executed for the crime, all within two weeks.

According to Indian culture however, Weequehela’s action had been justified, and the Delaware Indians viewed his death as murder. In 1728, his kinsman Menakihikon, a Munsee sachem, made a failed attempt to raise both the Miami and Iroquois League against the English. As late as 1757, Teedyuscung stilled hearkened to the death of Weequehela as a reason why the Delaware went to war against the English at the outbreak of the French and Indian War.

From the records of the time it is clear that several prominent Indians of both the Cranbury and Bethel groups were related to Weequehela; Sara Store was identified as his widow at the 1758 Crosswicks conference, Tom Store was identified as his cousin at the 1757 conference at Easton, and Andrew Woolley had signed as Weequehela’s sister’s son at the same time. An 1864 letter written by Weequehela’s great-great granddaughter identified Bartholomew Calvin as his grandson (making Stephen Calvin, the schoolmaster at Bethel and later Brotherton, the son-in-law of Weequehela. Calvin’s wife’s name was Mary).  ^{The Calvin family played a prominent role at Brotherton, and in the subsequent removals to Wisconsin by the 1830s.}

As a consequence of the disputed Indian land claims presented at Crosswicks in 1758, the Indian Commissioners were empowered to purchase all of the Indian claims to these lands, and, in return, those Indian claimants would give up all of the said parcels (with a few exceptions). In August 1758 at the Treaty of Easton, New Jersey agreed to acquire a tract of land to be set aside as a permanent Indian reservation. In March 1759 the colony purchased land at Edgepillock, Burlington County which Governor Bernard named Brotherton. The governor asked Brainerd to resume his role as missionary, and with the approval of the Presbyterian Synod of Philadelphia the minister once again joined his Indian charges. He moved to Brotherton in November 1759 and was associated with that community until his death in 1781.

For fourteen years, from 1746 to 1760, Bethel was an important mission community of Delaware Indians. It was part of the ongoing efforts of colonial leaders, both religious and secular, to provide a stable existence where both Christianity and Anglo-American culture could be inculcated into Native American society. It also was part of the defacto relocation of indigenous people across an ever-changing landscape. While Thomas Store, Andrew Woolley, and John Pumpshire moved to Brotherton, other Bethel residents, including Isaac Still and Joe Peepy, moved to the Indian communities in the Susquehanna valley. Still returned to Bucks County, Pennsylvania, where he led sixty Delawares to the west in October, 1775. In May, 1776, he died of small pox while returning to the Ohio country from a diplomatic mission to Congress. Joe Peepy and his family had become Moravian converts, and were amongst the victims of the Gnadenhutten Massacre in 1782.

In 1801, forty-two years after the establishment of Brotherton, the State of New Jersey acted to dissolve the reservation, and its residents removed to New Stockbridge, New York, where the Stockbridge Mohicans of Massachusetts had settled after the American Revolution. This group of Delawares migrated with the Stockbridge Mohicans to Indiana and eventually to Wisconsin where they remain today as part of the Stockbridge-Munsee Community of Mohicans.