As the settlement began to grow and expand new tensions surfaced. Finally in 1647, following the construction of houses east of the original village at "Old Town," Thomas Halsey's wife was murdered by Indians. The facts in the case were never recorded, but it appears that Mandush and the ocher Shinnecock headmen refused to cooperate with the settlers in an investigation of the incident. The town quickly turned into an armed camp. Wyandanch was sent from Montauk by Lion Gardiner to negotiate a settlement. It seems chat as a part of the agreement, the Shinnecock were forced to acknowledge Wyandanch as their "grand sachem". The arbitrary nature of this action is underscored by the wording in the 1640 deed regarding the authority of the Shinnecock headmen. The 12 Shinnecock men mentioned in the deed were referred to as " . . . the native inhabitants and true owners of the Eastern part of Long Island. This title carried with it the authority to sell Shinnecock lands in the future. The puppet was now in place. The English had their man and they exploited him ruthlessly as the "deed game" continued.

If the Shinnecock were at all unclear about English concepts of property, they were forcefully instructed by the Southampton settlers after some disagreements about land rights in 1649. The Indian concept of land use was clearly challenged here. The Indians appear to have taken the view chat the deed had given the English the right to use as much land as they needed. Any land that the English did not occupy and plant would therefore be available for Indian use. The Indians had planted on unused land west of the village. The English demanded that this practice be halted and asserted the right to tell the Indians where they could plant. This agreement raised, at the same 1640 deed. It appears that even the English were unclear about the "islands" of Indian lands in the area between the town and Canoe Place. The deed granted to the English all the lands lying eastward from Canoe Place including the "old ground formerly planted lying eastward from the first creek at the westrnore end of Shinnecock plaine." Yet in the 1649 agreement they clearly make reference to Indian land within this same area. Did the Indians retain title to the land where their villages were located and to some planting fields? The implication of this "planting" is that the Indians retained title in the English sense of the term to some land between the English town and Canoe Place.

This same issue is also raised by an entry in the town records for October 6, 1642. It was ordered that no settler could ". . . buy any land of Indians within the bounds of the town without consent of the General Court". This order clearly indicates that some of the land within the town "bounds" still belonged to the Indians. The reference to the "General Court" may have been to the Government of Massachusetts Bay Colony because the town did not unite with Connecticut until 1644. It is also possible that the "General Court" was simply the local town government.

Another confusing peculiarity of the 1640 deed is the absence of a clearly defined eastern boundary. The document simply says:

all the lands lying eastward between the foresaid bounds by water (the ocean and Peconic Bay) to wit, all the land pertaining to the parteyes aforesaid, as alsoe all the old ground formerly planted lying eastward from the first creek at the westemore end of Shinnecock plane...