As the Puritans continued to colonize New England, localized Indian uprising were fairly common as they became displaced. The Pequots of New England were annihilated in 1637 by Massachusetts and Connecticut troops, however, and most uprisings ceased.

Initially welcoming and peaceful toward the Puritans (see Plymouth Colony), the Indians were soon displaced from their land, and were forced to accept missionaries interfering in their affairs. In 1675, the Wampanoag sachem Metacom (known as King Phillip in England) launched a massive attack against the Puritans in an attempt to save his people's way of life. King Phillip organized a great army which included disgruntled members of other New England tribes. His armies obliterated White settlements near Plymouth and in western Massachusetts.

The White settlers responded with brutal force and more or less exterminated all of the original New England Indian tribes. King Phillip's War provided the template for which rationale for Indian displacement was conceived - White settlers provoking Indians to war by systematically invading and stealing their land and then annihilating them when the Indians responded with violence.

In response to the Indian annihilation in Massachusetts, as well as various acts of insubordination such as intolerance toward other sects, coining money without the crown's permission, and the failure to enforce the 1660 Navigation Act (Certain goods such as Tobacco and Sugar could only be exported to European countries by way of England), Charles II revoked the Massachusetts Bay Colony.