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After the death of Oliver Cromwell, Haynes supported the Wallingford House party when they overthrew Richard Cromwell and in 1659 introduced the short lived second Commonwealth. In December, shortly before the Restoration, the Rump Parliament ordered him to leave London and return home, but he chose not to. In November 1660 he was arrested on suspicion of subversion, and held in the Tower of London for 18 months. He was released in April 1662 upon payment of a £5,000 bond for his future good behaviour. He retired to his family estate of Copford Hall and lived quietly until his death on 26 August 1693.