On December 15, 1860, he was dispatched by the state of Mississippi to South Carolina as a secession commissioner.
He became lieutenant and later captain in the First Regiment of Mississippi Light Artillery, losing an arm at the siege of Vicksburg.
Hooker was elected Attorney General of Mississippi in 1865 and the same year was removed with the other officers of the state by the U.S. military authorities.
Unusual for a southern congressman of that era, Hooker spoke positively about some of the racial change the Civil War had brought, declaring that the former slave had become "a full-fledged American citizen .
He maintained that allotment would cause citizens of Native American nations to lose their land “and all the proceeds from the sale of it by fraud, force, or violence.”[5] The allotment reforms ultimately were ratified in the Dawes Act of 1887 which, as Hooker presaged, resulted in the loss of 86,000,000 acres of Native American territory nationwide between 1887 and 1934.