After numerous arrests for theft and similar offenses, Haggerty and Schuylkill Ranger Hugh Murphy were convicted of the robbery of a Ninth Street store and sentenced to ten years imprisonment on December 12, 1865. He was pardoned by Governor Andrew G. Curtin eight months later, in part to Haggerty's political connections and his promise to leave the country upon his release, and lived in Canada for a brief time before returning to the city to resume his criminal career. Haggerty remained a major underworld figure in Philadelphia until January 1869 when he was arrested on several counts of assault with intent to kill; during his arrest, he shot the arresting police officer. He was caught trying to escape from prison but was later released on bail and fled the city. Staying in New York City for a brief time, he returned to Philadelphia in April to surrender himself to authorities after the wounded police officer had received "hush money". He won both court cases against him but was ordered at the second trial to return to the Eastern State Penitentiary by the District Attorney for violating the terms of his release. While his lawyers argued the ruling, Haggerty disappeared from the courthouse during a recess in what was suspected to have been a planned escape.