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] The famous Toleration Act of 1649 was passed at the first assembly succeeding Stone's appointment.

It was very probably in great part a copy of a bill in the code of sixteen laws which Baltimore sent over at this time, and it very nearly repeated the provisions of the oath required of Governor Stone.

While the terms of the act did not place the right on that broad plane of universal principle stated later in the Virginia Declaration of Rights, it proclaimed toleration, even if it was a toleration of a very limited nature.[27] Stone had recommended himself to Calvert by promising to lead five hundred persons of British or Irish descent[28] into Maryland; and this engagement he was soon able to perform through the Puritans, whose story of persecution in Virginia has been already related.