 On September 5, he mustered out of the 1st California Infantry and joined up with the 1st New Mexico Infantry at Santa Fe, becoming a lieutenant colonel on February 5, 1865.In January 1866 Willis was in command of Fort Selden when he heard a rumor that a large band of Apaches had sacked the Janos presidio in Chihuahua.Hastily he organized an expedition of fifty infantrymen and twenty-five cavalrymen to march to the aid of the Mexican citizens there.