Accordingly in 1639 the assembly met and passed various acts, mostly relating to civil affairs. One, however, was specially noteworthy, as giving to the "Holy Church" "her rights and liberties," meaning by this the Church of Rome, for, as Gardiner says, the title was never applied to the Church of England. It was at the same time expressly enacted that all the Christian inhabitants should be in the enjoyment of every right and privilege as free as the natural-born subjects of England. If Roger Williams was the first to proclaim absolute religious liberty, Lord Baltimore was hardly behind him in putting this into practice. As has been neatly said, "The Ark and the Dove were names of happy omen: the one saved from the general wreck the germs of political liberty, and the other bore the olive-branch of religious peace."
During the civil war in England the affairs of Maryland were in a very disturbed condition. Clayborne, Maryland's evil genius, seized the opportunity to foment an insurrection, possessed himself once more of Kent Island, and compelled the governor to flee to Virginia. Returning in 1646, Calvert was fortunate enough to recover the reins of government, but the following year witnessed the close of his administration and his short though useful and eventful life. Few men intrusted with almost absolute authority have exercised it with so much firmness and at the same time with so much ability, discretion, and uprightness.
His successor, Greene, a Catholic, was not likely to find favor with the Puritan Parliament of England, and Baltimore, in 1648, to conciliate the ruling powers and to refute the charge that Maryland was only a retreat for Romanists, removed the governor and appointed instead one who was a Protestant and a firm supporter of Parliament. The council was also changed so as to place the Catholics in the minority. The oath of the new governor restrained him from molesting any person, especially if of the Roman Catholic persuasion, on account of religious profession. The way was thus opened for the Act of Toleration passed in 1649.
This law, after specifying certain speeches against the Trinity, the Virgin, or the saints as punishable offences, declared that equal privileges should be enjoyed by Christians of all creeds. Whatever the motives of Baltimore, his policy was certainly wise and commendable.
A new and troublesome element was now introduced into the colony. Some Puritans who had not been tolerated among the stanch Church-of-England inhabitants of Virginia were invited by Governor Stone to Maryland. Their home here, which they named Providence, is now known as Annapolis.The new-comers objected to the oath of fidelity, refused to send burgesses to the assembly, and were ready to overthrow the government whose protection they were enjoying. Opportunity soon offered. Parliament had already in 1652 brought Virginia to submission. Maryland was now accused of disloyalty, and when we notice among the commissioners appointed by the Council of State, the name of Clayborne, it is not difficult to understand who was the author of this charge. The governor was removed, but being popular and not averse to compromise, was quickly restored. Then came the accession of Cromwell to power as Protector of England. Parliament was dissolved. The authority of its commissioners of course ceased. Baltimore seized this opportunity to regain his position as proprietary. He bade Stone to require the oath of fidelity to the proprietary from those who occupied lands, and to issue all writs in his name. He maintained that the province now stood in the same relations to the Protectorate which it had borne to the royalist government of Charles I.
So thought Cromwell, but not so Clayborne or the Maryland Puritans. They deposed Stone, and put in power Fuller, who was in sympathy with their designs. There resulted a reversal of the acts of former assemblies, and legislation hostile to the Catholics. The new assembly, from which Catholics were carefully excluded by disfranchisement, at once repealed the Act of Toleration. Protection was withdrawn from those who professed the popish religion, and they were forbidden the exercise of that faith in the province. Severe penalties were threatened against "prelacy" and "licentiousness" thus restricting the benefits of their "Act concerning Religion" to the Puritan element now in power. The authority of the proprietary himself was disputed, and colonists were invited to take lands without his knowledge or consent.
Baltimore adopted vigorous measures. By his orders Stone made a forcible attempt to regain control of the province, but was defeated at Providence and taken prisoner. His life was spared, but four of his men were condemned and executed. Baltimore again invoked the powerful intervention of Cromwell, and again were the enemies of Maryland sternly rebuked for their interference in the affairs of that province, and told in plain language to leave matters as they had found them. In 1656, after an inquiry by the Commissioners of Trade, the claims of Baltimore were admitted to be just, and he promptly sent his brother Philip to be a member of the council and secretary of the province. The legislation of the usurping Puritans was set aside, religious toleration once more had full sway, and a general pardon was proclaimed to those who had taken part in the late disturbances.In the meantime, Fendall, who had been appointed governor by Baltimore, plotted to make himself independent of his master, and, with the connivance of the assembly, proceeded to usurp the authority which was lawfully vested in the proprietary. But the attempt was a miserable failure. Philip Calvert was immediately made governor by the now all-powerful proprietary, who had the favor and support of Charles II., just coming to the throne. Peace and prosperity came back to the colony so sorely and frequently vexed by civil dissensions. The laws were just and liberal, encouraging the advent of settlers of whatever creed, while the rule of the Calverts was wise and benign, such as to merit the respect and admiration of posterity. In 1643 Virginia and Maryland together had less than twenty thousand inhabitants. In 1660 Maryland alone, according to Fuller, had eight thousand. Chalmers thinks there were no fewer than twelve thousand at this date.