During these tumults so many persons went over from Virginia to Maryland that the Virginia assembly sent Captain Edward Hill and Captain Thomas Willoughby to compel the return of the absentees,[20] with curious result.  As the province was without a governor, some of the council of Maryland issued, in the name of the refugee Calvert, a commission to Hill to act as governor of Maryland.  The revolutionists flattered themselves that a stable government under a Protestant governor was now at hand.  But the unexpected came to pass, when, in December, 1646, Governor Calvert suddenly appeared with a strong body of soldiers furnished by Sir William Berkeley and re-established his authority by capturing both Hill and the Protestant assembly then sitting at St. Mary’s.

These two years of civil war in Maryland are called the “plundering time.”  Claiborne again appears, though there is no evidence that he had any part in Ingle’s spoliations.[21] He did visit Kent Island about Christmas, 1645, and put Captain Brent, to whom Governor Calvert had assigned his house and property, in a terrible fright.  One year later he visited the island a second time, when he offered to aid the Kent Islanders in marching upon St. Mary’s with a view of reinstating Hill.  When the men of Kent declined to take the risk, Claiborne returned to Virginia, and Kent Island fell once more under the government of Lord Baltimore.[22] On this visit Claiborne, instead of posing as a friend of the Parliament, showed a commission and letter from the king, by whom he appears to have stood till the king’s death in 1649.  Charles I., in his turn, who deposed Lord Baltimore as a “notorious parliamentarian,” appointed Claiborne, in 1642, treasurer of Virginia;[23] and Charles II. included his name among the list of councillors in the commission issued by Sir William Berkeley in 1650.[24]

While Maryland was thus convulsed with civil war an ordinance settling the Maryland government in Protestant hands passed the House of Lords.  Before the Commons could concur, Lord Baltimore appeared and asked for time to inquire into the charges.  This was after the battle of Marston Moor, and perhaps marks the moment when Lord Baltimore, conceiving the king’s cause desperate, began to trim his sails to the parliamentary side.  His request was granted, and Parliament, diverted from immediate action, left Baltimore’s authority unaffected for several years.[25]

In this interval Baltimore busied himself in reorganizing his government on a Protestant basis.  Leonard Calvert died in June, 1647, not long after his coup d’etat at St. Mary’s, and upon his deathbed he appointed Thomas Greene, a Catholic and royalist, as his successor.  Lord Baltimore removed him and appointed in his stead a Protestant, Captain William Stone, of Northampton County, Virginia, giving him a Protestant secretary and a Protestant majority of councillors.  Yet Baltimore took care not to surrender the cardinal principle of his government.  Before Stone and his chief officers were allowed to take office they were required to swear not to “molest any person in the colony professing to believe in Jesus Christ for or in respect of his or her religion, and in particular no Roman Catholic."[26]