His time in office was very short, because the new English king, James II put most of the American colonies under a single royal governor, Edmund Andros, and Rhode Island fell under the Dominion of New England for three years.

The flight of King James II to France in 1689, and the subsequent ouster of Andros from New England, brought about the restoration of Rhode Island's government under the Royal Charter of 1663, but Clarke refused to serve as governor.

[2] In 1667 Clarke was elected as a Deputy to the General Assembly from Newport, launching a public career that would span nearly half a century.

[4] Most of the settlers on the mainland (Providence and Warwick) fled to Aquidneck Island where Newport and Portsmouth were located.

[4] A flotilla of sloops, or gunboats, each with five or six men, sailed constantly around the island to ward off possible attackers.

[5] Since the Rhode Island colony was about half Quaker during this timeframe, a 1673 law was enacted exempting men from military duty if bearing arms was against their consciences.

[7] Joseph Dudley and his council held court at Narragansett in June 1686, making the territory, named King's Province, independent of any colony.

[8] One favorable outcome of the Andros' regime was the eventual return to Rhode Island of the formerly disputed Narragansett country claimed by Humphrey Atherton and his company.

[8] In 1689 King James fled to France, after which William III and Mary II ascended to the throne of England.

[7] Andros was ousted from New England, and the Royal Charter of 1663 once again became the governing document of the Rhode Island colony.

[9] A plot to assassinate England's Protestant King William III was revealed, and the colonies were preparing for an invasion by France.

[9] The Assembly replied with a letter explaining that the Rhode Island colony had a long coastline and was very exposed and under-defended by forts, and could not possibly offer assistance.