W/Cmdr C. A. T. Jones was posted to 66 Squadron flying Gloster Gauntlets and he was with the squadron when it received its first Spitfire in August 1938.
In April 1940 he was commissioned and posted to 611 Squadron. On 2nd June, he probably destroyed a Bf 109 over Dunkirk.

On 29th August, 1940, he was posted to 312 Squadron, as a Flight Commander. The squadron was formed on that day at Duxford.

He moved to 616 Squadron on 4th September, again as a Flight Commander.
He flew 32 sorties and claimed two Bf 109s.
On 5th November, 1940, he was badly wounded in the right elbow by return fire from a He 111 engaged off Spurn Head, but he managed to return to base. The enemy aircraft crashed into the Humber and Jones was Mentioned in Despatches for flying the aircraft back safely with just one arm. His injuries prevented him flying for eleven months, but during this time he commanded a Sector Operations Room.
He returned to flying as a Flight Commander with 601 Squadron flying Bell Airacobras, later becoming the Squadron Commander.

From February 1942, until February 1944, Jones commanded 79 Squadron, mostly in India but also in Burma. During this time he shot down 2 Mitsubishi bombers. He was awarded the DFC (14/4/44).