When the unit was originally mustered out of service, the 90-day enlistment terms having expired, Nugent accepted a commission as a captain in the regular army. He was immediately assigned to the 13th Infantry Regiment whose commanding officer, Colonel William Tecumseh Sherman, personally requested. Taking a leave of absence to return to New York, he assisted Thomas Francis Meagher in organizing the Irish Brigade. The newly reformed 69th Infantry Regiment was the first unit assigned to the Irish Brigade and, with Nugent as its colonel, he led the "Fighting 69th" at the Battles of Fair Oaks, Gaines Mill, Savage Station, White Oak Swamp, Glendale, and Malvern Hill.