Military command and governorship
From 1663 to 1673, Leverett held the rank of major-general of the Massachusetts militia, and was repeatedly elected as a deputy to the general court or to the council of assistants. During this time he oversaw the strengthening of Boston's defenses. He was also again sent to the colonial settlements of New Hampshire and southern Maine, where some colonists had objected to Massachusetts rule and arrested colonial officials.
Following the restoration of Charles II to the throne, all of England's colonies came under his scrutiny. In 1665, the Carr-Cartwright Commission visited Massachusetts. They were instructed to gain the colony's agreement to terms demanded by Charles in a letter he sent to the colonial government in 1662, in which he instructed the colony to adopt more tolerant religious laws, and to enforce the Navigation Acts. The arrival of the commissioners was of some concern to the government, and Leverett was placed on a committee to draft a petition to the king demanding the commission's recall. The document they drafted characterized the commissioners as "agents of evil sent to Massachusetts to subvert its charter and destroy its independence."
In 1665, those four commissioners validated a previous 1662 royal ruling which declared Massachusetts had no authority over Maine. When the commissioners left New England in 1668, Leverett led a counter-coup against the government established in Maine by them in order to reassert Massachusetts authority. On July 14, 1668 he, Richard Waldron, Edward Tyng (father of Edward Tyng, Robert Pike and 12 cavalrymen rode into York, Maine and deposed the officials and swore in new military officers and court officials.
Leverett served as deputy governor under governor Richard Bellingham from 1671 to 1672, and succeeded to his position after the governor's death. His tenure as governor was chiefly notable because of King Philip's War, and the rising threats to the colonial charter that culminated in its revocation in 1684. The colony angered the king by purchasing the claims of Sir Ferdinando Gorges to portions of Maine in 1677, a territory Charles had intended to acquire for his son, the Duke of Monmouth. Edward Randolph, sent by Charles to report on the New England colonies, reported in 1676 that Leverett believed the colony to be beyond the crown's reach: "He freely declared to me that the laws made by your Majesty and your Parliament obligeth them in nothing but what consists with the interest of that colony".
Although Leverett favored religious tolerance, there were still many in the colony who did not. Baptists were able to openly begin worship in Boston during his tenure, but he has also been criticized by Quaker historians for harsh anti-Quaker laws passed in 1677. The Baptists' time in Boston did not last, and they were thrown out in 1680 after Simon Bradstreet became governor.