1647 Sir Thomas Fairfax ordered his regiment into London to seize money for paying the troops. When the Second English Civil War began in April 1648, Hewson helped suppress the rebellion in Kent, including the storming of Maidstone, where he was commended for his bravery. The renewed fighting convinced Cromwell and others that Charles must be removed, and Hewson played a prominent part in bringing this about. His regiment supported Pride's Purge of December 1648, where MPs who opposed putting the king on trial were forcibly excluded or arrested. In January 1649, he served on the court that approved the Execution of Charles I, signed the death warrant and reportedly sourced the headsman, while soldiers from his regiment under Daniel Axtell provided security during the trial and execution. Despite his religious radicalism, Hewson was an authoritarian in matters of army discipline. When 300 men from his regiment refused in May 1649 to serve in the proposed Cromwellian Conquest of Ireland, they were swiftly dismissed, after which Hewson helped Cromwell crush the Banbury mutiny. In late August, he arrived in Ireland as part of Cromwell's expeditionary force and was present at the Siege of Drogheda, where he allegedly set fire to a church containing nearly 100 Irish and English Royalist refugees. Shortly afterwards, Hewson replaced Michael Jones as Governor of Dublin, then participated in the relief of Arklow and the Siege of Kilkenny in March 1650, where he lost an eye. The Interregnum and death After the capture of Clonmel in May 1650, Cromwell returned to England, leaving Henry Ireton in charge of reducing the remaining pockets of organised Irish resistance. Hewson continued as Governor of Dublin, and joined the Gathered church founded there by John Rogers, a leading Fifth Monarchist preacher, putting him at odds with the majority of the Dublin Castle administration, who were either Presbyterians or members of the mainstream Protestant Church of Ireland. Recalled to London for consultations in 1652, he was nominated MP for Ireland in the 1653 Barebones Parliament; unlike many of his army colleagues, he supported its dissolution, and backed Cromwell's appointment as Lord Protector, albeit allegedly with great reluctance. Returning to Ireland, Hewson was elected MP for County Dublin in the First Protectorate Parliament of 1654, but later fell out with Henry Cromwell, the new Lord Lieutenant of Ireland. Ordered back to England in 1656, he represented Guildford in the Second Protectorate Parliament,