English colonies tended to be organized along one of three lines: they could be either corporate, proprietary or royal colonies. Corporate colonies were run and administered by a Joint Stock Company while proprietary colonies were run and administered by a single owner. (In both cases, they would be governed by a charter issued by the crown.) Finally, a royal colony was run by a royal governor who answered directly to the monarchy. Taken as a whole, the general pattern of English colonization was one by which a colony would be founded as either a proprietary or a corporate colony, only to be later reorganized as a royal colony.
Even before King James II ascended to the throne, the Massachusetts colony had already recently had its charter revoked. However, under the new king, the colonies that made up New England would be consolidated together to create a single colony known as the Dominion of New England, to be run by royal governor. This represented a radical transformation in colonial government, and one deeply unpopular in the colonies themselves.
However dramatic this reorganization might have been, it turned out to be short lived. Keep in mind, James II's rule in England was a short one. Ascending to the throne after his brother's death in 1685, he only reigned until 1688, when he was driven from power by the Glorious Revolution. This turn of events would inspire acts of rebellion within the colony. With William and Mary ascending to the throne, the Dominion of New England was soon afterward be dissolved.