In early 1945, he escaped from the Granite Reformatory with a number of other prisoners, but was recaptured in April 1945 and sentenced to an additional 99 years for kidnapping a man, Jack Nance, while he was on the run.

He was then sent to Leavenworth, but attempted to escape while in the custody of the United States Marshals Service and was transferred to Alcatraz along with an additional five-year sentence.

He claimed that he had received a postcard from Frank Morris and the Anglin brothers, John and Clarence, which read "Gone fishing", which was a code word that their escape had succeeded.

He died of AIDS-related complications[citation needed] on October 3, 1988, at the Medical Center for Federal Prisoners in Springfield, Missouri,[5] and was buried in a paupers' grave.

"Whitey" Bulger, who had befriended Carnes while on Alcatraz, paid for his body to be exhumed and reburied on land in the Choctaw Nation of Oklahoma.

Carnes' life was interpreted in Rolling Way the Rock, a performance piece by Tim Tingle, also a Choctaw man, which premiered in 2006 at the International Symposium of Artists of Conscience in Victoria, British Columbia.