Murtagh was holed up with Fergus and Marsali, and he was searching for information on Stephen Bonnet on top of his efforts as a Regulator.
He and Fergus finally got word of where Bonnet was staying after arriving in Wilmington, and they managed to take him by surprise and capture him.
As of “if Not For Hope,” more than just the redcoats were on the lookout for Murtagh, as signs were posted with Murtagh’s picture, advertising a reward “to any person who shall seize and secure the person known as MURTAGH FITZGIBBONS.”