With Thomas dead, there was nobody who could either implicate or clear Henry Percy of any involvement in the plot. His failure to ensure that Thomas took the Oath of Supremacy upon his appointment as a Gentleman Pensioner, and their meeting on 4 November, constituted damning evidence, and the Privy Council also suspected that had the plot succeeded, he would have been Princess Elizabeth's protector. With insufficient evidence to convict him he was charged with contempt, fined £30,000 and stripped of all public offices. He remained in the Tower until 1621.
