At the conclusion of the First English Civil War, Peter, though greatly disliked by the Presbyterians and the Scots, had attained great influence as leader of the Independents. In his pamphlet "Last Report of the English Wars" (1646), he urged religious toleration, an alliance with foreign Protestants, and an active propagation of the gospel. In the dispute between the New Model Army and the Long Parliament he naturally took the side of the former, and after the seizure of the King by the Army in June 1647 had interviews with Charles I at Newmarket and Windsor, in which he favourably impressed the latter, and gave advice upon the best course to pursue. He performed useful services in the Second Civil War, procured guns for the besiegers at the siege of Pembroke, raised troops in the Midlands, and arranged the surrender of the Duke of Hamilton at Uttoxeter. When the Army entered London in 1648 he was one of the few preachers who supported the move and spoke out in support of Pride's Purge. In August 1649 he accompanied Cromwell on his Irish Campaign, and was present at the fall of Wexford, while later he assisted the campaign by superintending from England the despatch to Cromwell of supplies and reinforcements, and was himself destined by Cromwell for a regiment of foot. In 1650 he was appointed chaplain to the Council of State. Through his office he exerted influence on various committees concerned with religious, legal and social reforms. The same year, during the Third Civil War he was in South Wales, endeavouring to bring over the people to the cause, and subsequently was present at the Battle of Worcester in 1651, where afterwards he preached to the victorious Parliamentary soldiers.