When World War II broke out, he departed Africa, due to the circumstances of military presence of Nazi Germany forces.
While working in the Canal Zone, he applied for a commission in the United States Marine Corps upon the suggestion of his brother, William K. Jones.
He became the commanding officer of the Amphibious Corps, Pacific Fleet's (ACPF) Amphib Recon Company on January 7, 1943.
Putting ashore from the submarine USS Nautilus, Jones and the V Amphibious Corps Reconnaissance Company attacked and took the Japanese-held atoll of Abemama during Operation Boxcloth, part of the larger U.S. effort to seize the Gilbert Islands in November 1943.
[6] After spending 25 months of combat duty in the Pacific during World War II from 1943 to 1945, Major Jones was awarded several commendations.