When Harvey heard of these proceedings he was greatly enraged. Summoning the Council to meet without delay, he issued warrants for Dr. Pott and several others that had aided in circulating the petition. "After a few days Potts was brought up prisoner, having before his apprehending bin in the lower parts of the Country there also mustering his names at a meeting called for that purpose."[288] He does not seem to have feared the angry threats of the Governor, for when put in irons and brought before the Council, he readily consented to surrender the offending petition. At the same time he asserted "that if he had offended he did appeal to the King, for he was sure of noe justice from Sir John Harvey". When some of the other prisoners, in their hearing before the Council, asked the cause of their arrest, the Governor told them they should be informed at the gallows.

Shortly after this the Council was summoned to deliberate on the fate of the accused. The Governor, fearing that he might not secure conviction from a jury, "declared it necessary that Marshall law should be executed upon" them. When the Councillors refused to consent to any other than a legal trial, Harvey flew into a furious passion. For a while he paced back and forth in the room hardly able to contain himself. At length he sat down in his chair, and with a dark countenance commanded his colleagues to be seated. A long pause ensued, and then he announced that he had a question that they must answer each in his turn, without deliberation or consultation. "What," he enquired, "doe you think they deserve that have gone about to persuade the people from their obedience to his Majesties substitute?" "And I begin with you," he said, turning to Mr. Minifie. "I am but a young lawyer," Minifie replied, "and dare not uppon the suddain deliver my opinion." At this point Mr. Farrar began to complain of these strange proceedings, but Harvey commanded him to be silent. Captain Matthews also protested, and the other Councillors soon joined him in refusing to answer the Governor's question. "Then followed many bitter Languages from him till the sitting ended."

At the next meeting Harvey asked what the Council thought were the reasons that the petition had been circulated against him, and demanded to know whether they had any knowledge of the matter. Mr. Minifie replied that the chief grievance of the people was the detaining of the letter of the Assembly to the King. This answer seems to have aroused the Governor's fury, for, arising from his seat, and striking Mr. Minifie a resounding blow upon the shoulder, he cried, "Doe you say soe? I arrest you upon suspicion of treason to his Majesty." But Harvey found that he could not deal thus arbitrarily with the Councillors. Utie and Matthews rushed up and seizing him cried, "And we you upon suspicion of treason to his Majestie". Dr. Pott, who was present and had probably been waiting for this crisis, held up his hand as a signal to confederates without, "when straight about 40 musketiers ... which before that time lay hid, came ... running with their peeces presented" towards the house. "Stay here," commanded Pott, "until there be use of you."

In the meanwhile the Councillors crowded around Harvey. "Sir," said Matthews, "there is no harm intended you save only to acquaint you with the grievances of the Inhabitants and to that end I desire you to sit downe in your Chayre."

And there, with the enraged Governor seated before him, he poured out the recital of the people's wrongs. When he had finished there came an ominous pause. Finally Matthews spoke again. "Sir," he said, "the peoples fury is up against you and to appease it, is beyond our power, unlesse you please to goe for England, there to answer their complaints." But this Harvey refused to do. He had been made Governor of Virginia by the King, he said, and without his command he would not leave his charge.

But before many days the Governor changed his mind. He found himself deserted by all and entirely in the power of the Councillors. As sentinals were placed "in all wayes & passages so that noe man could travell or come from place to place", he could make no effort to raise troops. Dr. Pott and the other prisoners were set at liberty. A guard was placed around Harvey, ostensibly to protect him, but really with the purpose of restraining him. A letter came from Captain Purifee, a Councillor then in the "lower parts" of the colony, which spoke of designs of the people to bring Harvey to account for his many wrongs. In alarm the Governor consented to take the first ship for England. He endeavored, however, to name his successor, to induce Matthews, Pierce, and Minifie to go with him to England, and to secure a promise from the Council not to molest Maryland. But they would consent to none of these things.

In the meantime an Assembly had been called to consider the innumerable grievances against the Governor. When they met at Jamestown, Harvey sent them a letter, declaring the session illegal and ordering them to disperse to their homes. "Notwithstanding his threats ... the assembly proceeded according to their former intentions." Harvey then dispatched a letter to the Council, ordering them to send him his royal commission and instructions, but these documents had been intrusted to the keeping of Mr. Minifie with directions not to surrender them. The Council then turned themselves to the task of selecting a successor to Harvey. Their unanimous vote was given to Captain Francis West, the senior member of the board and formerly Governor. Feeling that since the expulsion of Harvey had been primarily a movement to protect the rights of the people, the Burgesses should have some voice in the election of the new Governor, they appealed to the Assembly for the ratification of their choice. West was popular in the colony, and "the people's suffrages" were cast for him as willingly as had been those of the Council. The Assembly then drew up resolutions setting forth the misconduct of Harvey and justifying their course in sending him back to England. These documents were entrusted to one Thomas Harwood, who was to deliver them to the King. Of what happened after Harvey's departure we have little record, but it is probable that the colonists revenged themselves upon the deposed Governor by confiscating all his ill gotten possessions.

It was decided that Dr. Pott should go to England to stand trial as his appeal to the King had taken the case beyond the jurisdiction of the Virginia courts. He and Harwood sailed upon the same vessel with Sir John. It is not hard to imagine with what dark looks or angry words Pott and Harvey greeted each other during their long voyage across the Atlantic. Doubtless Harwood and Pott held many a consultation upon what steps should be taken when they reached England to secure a favorable hearing for the colony, and to frustrate Harvey's plans for revenge. It was Harwood's intention to hasten to London, in order to forestall the Governor and "to make friends and the case good against him, before he could come".[289] But Sir John was too quick for him. Hardly had the ship touched the dock at Plymouth, than he was off to see the mayor of the city. This officer, upon hearing of the "late mutiny and rebellion" in Virginia, put Pott under arrest, "as a principal author and agent thereof", and seized all the papers and letters that had been entrusted to Harwood. Having thus gotten his hands upon the important documents, Harvey proceeded to London to complain of the indignities shown him and to ask for the punishment of his enemies.

When Charles I learned that the Virginians had deposed his Governor and sent him back to England, he was surprised and angered. It was, he said, an assumption of regal power to oust thus unceremoniously one of his officers, and he was resolved to send Harvey back, if for one day only. And should the Governor acquit himself of the charges against him, he was to be inflicted upon the colony even longer than had at first been intended. The case came before the Privy Council in December 1635.[290] In the charges that were made against Harvey nothing was said of the illegal and arbitrary measures that had caused the people to depose him. All reference was omitted to the detaining of the Assembly's letter, to the support given Maryland, to the abuse of the courts, to illegal taxes and proclamations. Possibly the agents of the Virginians felt that such accusations as these would have no weight with the ministers of a monarch so little in sympathy with liberal government, so they trumped up other charges to sustain their cause. Despite the assertion of Harwood that Harvey "had so carryed himself in Virginia, that if ever hee retourned back thither hee would be pistolled or Shott", he was acquitted and restored to his office. West, Utie, Matthews, Minifie and Pierce, whom Harvey designated as the "chief actors in the munity", were ordered to come to England, there to answer before the Star Chamber the charge of treason.[291]

As the time approached for him to return to Virginia, Harvey began to show symptoms of nervousness. Feeling possibly that the threats of "pistolling" were not to be taken lightly, he requested the King to furnish him a royal vessel in which to make the journey. The appearance of one of the King's own ships in the James, he thought, would "much abate the bouldness of the offenders". This request was granted, and, after some months of delay, Harvey set forth proudly in the Black George. But Charles had not cared to send a really serviceable vessel to Virginia, and for a while it seemed that the Black George would relieve the colonists of their troubles by taking Sir John to the bottom. The vessel, it would appear, sprang a leak before it had been many hours at sea, and was forced to return to port. The Governor then decided that a merchant vessel would suffice for his purposes, and set sail again, upon a ship of the Isle of Wight.