He was the leader of the "popular party", a faction in the Massachusetts House that resisted encroachment by royal officials on colonial rights embodied in the Massachusetts Charter.

Cooke was elected to the commission of counsellors in May 1693; however, Governor Sir William Phips refused to ratify the choice, to exact revenge on Cooke's having opposed his appointment as chief magistrate.

Cooke was a confidential adviser of Lord Bellomont, who became Governor of Massachusetts in 1699.

[2] This had occurred after the 1689 Boston revolt, which deposed Sir Edmund Andros, governor of the Dominion of New England, and other officials (including Dudley).

Cooke served on the rebel council that took power after the dominion's overthrow.