When Mathews and the Council attempted to dissolve the Assembly on April 1, 1658, the Burgesses answered that the Governor's action was illegal, and that they would remain and complete their work. Mathews refused to concede their point formally, though he declared his willingness to allow them to continue in fact while the dispute was submitted to the Lord Protector in England. The Burgesses declared his answer unsatisfactory. They demanded a specific acknowledgment that the House remained undissolved. Mathews and the Council finally agreed to revoke the declaration of dissolution, but still insisted on referring the dispute to the Lord Protector. The House rejected this answer as well, asserting that the present power of Virginia resided in the Burgesses, who were not dissolvable by any power extant in Virginia but themselves. They directed the High Sheriff of James City County not to execute any warrant but from the Speaker of the House. In addition, they ordered Col. William Claiborne, the Secretary of the Council, to surrender the records of the country into the hands of John Smith, the Speaker of the Assembly, on the basis of the Burgesses' declaration to hold "supreame power of this country."

That the House of Burgesses did not mean its actions to be in defiance of the power that existed in England, however, is shown by its agreement to proclaim Richard, son of Oliver Cromwell, Lord Protector when the Governor sent down, at the March 1659 session, an official letter from His Highness' Council requiring that it be done. Immediately after agreeing to proclaim Richard, the Burgesses decided to address the new Lord Protector for confirmation of the privilege granted to the Assembly, perhaps under the terms of Bennett's secret instructions, to elect its own officers. Although the Speaker of the House assured the Burgesses that the Governor was willing to join them in such a request, some of the Burgesses expressed a desire to hear the assurance from the Governor's own lips. Accordingly, he was sent for and, to the satisfaction of the Burgesses, "acknowledged the supream power of electing officers to be by the present lawes resident in the Grand Assembly." He promised to join them in requesting confirmation of these privileges from His Highness.

The Assembly, at this same session, passed an act electing Mathews Governor again for two years "and then the Grand Assembly to elect a Governour as they shall think fitt." The act was to be in force "until his Highness pleasure be further signified." William Claiborne was appointed Secretary of State on his acknowledgment that he received the place from the Assembly, and with the proviso that he should continue Secretary until the next Assembly or until the Lord Protector's pleasure should be further signified to the colony.

The Assembly of 1659 marks the high water point of local government in Virginia. Not only were the Burgesses supreme in matters of general legislation, compelling the Governor and Secretary to bow to their sovereign power, but in their home counties affairs were conducted much as the local justices saw fit. The Assembly of 1659 even authorized free trade with the Indians by anyone in any goods—even guns and ammunition. Never before had regulation on a point of such vital interest to the security of the colony been so utterly abandoned.

Recall of Sir William Berkeley by the Assembly, 1659-1660

Soon after the Assembly of March 1659 ended, Richard Cromwell resigned the reins of government in England. The English nation was again plunged into turmoil. Letters arriving in Virginia spoke of the people divided "some for one Government some for another." The prospect of London "burned into Ashes and the streets running with blood" was held a likely outcome of the divisions.

In the midst of this troublous situation, Governor Mathews died. The next Assembly met in March 1660. In a move that has astonished historians since that time it asked Sir William Berkeley, the royal Governor whom its former leaders had deposed, to govern Virginia again. No royal banners were unfurled; Charles II was not proclaimed King. The House of Burgesses, holding the supreme power in the colony, merely offered the governorship to the man who had been universally admired for his justice, humanity, and willingness to sacrifice his own interest to that of the colony.

Berkeley had been unwilling to disavow his loyalty to the Crown in 1652 and he was not prepared to do so now. He replied to the Burgesses' invitation by saying that he would not dare to offend the King by accepting a commission to govern from any power in England opposed to him. He urged them to choose instead a more vigorous man from amongst their own number. But he did offer to accept the governorship directly from the House of Burgesses if the Council would concur with the Burgesses in offering it to him. He promised that if thereafter any supreme power in England succeeded in re-establishing its authority in Virginia he would immediately lay down his commission and "will live most submissively obedient to any power God shall set over me, as the experience of eight yeares have shewed I have done." He would not refuse their call, he wrote, if they accepted his conditions, for "I should be worthily thought hospitall mad, if I would not change povertie for wealth,—contempt for honor."

The Council on March 21, 1660, unanimously concurred in the Burgesses' choice of Berkeley as Governor, and the King's loyal servant was thereupon installed in the office.

Some historians have seen the election of Berkeley as the signal for a royalist purge of the Parliamentary influences that were thought to have existed in the colony since 1652. A study of the membership of the House of Burgesses, Council, and county courts, however, shows a continuity of membership which extends from before the Parliamentary seizure of the colony until after the restoration of King Charles II. The evidence suggests that there was no violent division between royalists and Parliamentarians in Virginia. The people were Virginians first and royalists or Parliamentarians second. The solidarity of their political interests was a harbinger of the American independence that was slowly to mature in the next century.