Rushworth was re-elected MP for Berwick in the Third Protectorate Parliament. He completed his written histories of the period and dedicated them to Richard Cromwell. As Richard Cromwell was unable to continue the office established by his father as Lord Protector, by 1660 real power had shifted to the Council of State and Rushworth became Secretary of the council. He was re-elected MP for Bewick in the Convention Parliament in 1660. Negotiations were then undertaken with the son of Charles I to return to England as its king, subject to the rule of Parliament. When Charles II took to the throne and restored the monarchy, Rushworth was reassigned to the office of Treasury Solicitor. On 7 June 1660 he presented to the Privy Council certain volumes of its records, which he claimed to have preserved from plunder "during the late unhappy times", and received the king's thanks for their restoration. Reports were spread, however, of Rushworth's complicity in the late king's death, and he was called before the lords to give an account of the deliberations of the regicides, but professed to know nothing except by hearsay. Rushworth was not re-elected to the parliament of 1661, but continued to act as agent for the town of Berwick, although complaints were made that the king could look for little obedience so long as such men were agents for corporations. Later years In September 1667, when Sir Orlando Bridgeman was made lord-keeper, he appointed Rushworth his secretary. The colony of Massachusetts also employed him as its agent at a salary of twelve guineas a year and his expenses, but it was scoffingly said in 1674 that all he had done for the colony was 'not worth a rush'. Rushworth was elected MP for Berwick again in March 1679 for the First Exclusion Parliament and in October 1679 for the Second Exclusion Parliament. He was returned again in March 1681, Rushworth and seems to have supported the Whig leaders. Though he had held lucrative posts and had inherited an estate from his cousin, Sir Richard Tempest, Rushworth's affairs were greatly embarrassed. He spent the last six years of his life in the King's Bench Prison in Southwark, "where, being reduced to his second childship, for his memory was quite decayed by taking too much brandy to keep up his spirits, he quietly gave up the ghost in his lodging in a certain alley