During this time Johns's probationary commission was confirmed. He continued to serve as a flying instructor until August 1918 when he transferred to No. 55 Squadron RAF, at the time part of the Independent Air Force, a section of the Royal Air Force that had been formed for the purpose of bombing targets deep inside Germany. Casualties in the Independent Air Force were high and Johns' career flying strategic bombing missions was characteristically short, lasting only six weeks. On 16 September 1918 he was piloting one of six DH.4s on their way to bomb Mannheim when his aircraft was hit by anti-aircraft fire and he was forced to drop out of formation. He jettisoned his single bomb and turned for home, but was attacked by a number of Fokker D.VII fighters. During a lengthy but one-sided battle, Johns' observer and rear-gunner, Second Lieutenant Alfred Edward Amey, was badly wounded and the aircraft shot down. The victory was credited to Georg Weiner, the commander of Jagdstaffel 3. Johns and Amey were taken prisoner by German troops: Johns received a leg wound during the battle and was slightly injured in the crash, but Amey died of his injuries later that day. Johns remained a prisoner of war until after the Armistice of 11 November 1918.