Despite the clemency, Vane remained in the Tower, and the income from his estates was seized. He suffered the privations of the prison, and was unable to discharge debts that ran to £10,000. He was transferred to the Isles of Scilly in October 1661 in order to limit access to him by potential conspirators who might be scheming to free him. He continued to write, principally on religious themes, seeking to come to terms with the political state of affairs and his condition. According to "The People's Case Stated", written by Vane in this time, power originated with God, but resided primarily with the people: "The power which is directive, and states and ascertains the morality of the rule of obedience, is in the hand of God; but the original, from whence all just power arises, which is magistratical and co-ercitive, is from the will or free gift of the people, who may either keep the power in themselves or give up their subjection and will in the hand of another." King and people were bound by "the fundamental constitution or compact", which if the king violated, the people might return to their original right and freedom.