Now firmly on the side of Parliament, Theophilus was sent to London in October to raise fresh troops and money and was present at the Execution of Charles I on 30 January. This action led to an alliance between Ormond, the Confederation, the Laggan Army and Munro's Covenanters, with the objective of restoring his son Charles II. In early summer, Theophilus returned to Dublin and took part in the Battle of Rathmines, a decisive victory won by his brother Michael over the Ormond-Confederate alliance. After Oliver Cromwell landed with the main expeditionary force in August, Theophilus was left in Dublin; Michael accompanied Cromwell on his autumn campaign and died of disease in December.