On D-Day, Lt. Doohan landed at Juno Beach with the Canadian Forces. He later recalled of the day: "The sea was rough; we were more afraid of drowning than the Germans." Doohan personally shot two snipers and led his men through a field of anti-tank mines to higher ground where they dug in for the night. Doohan was passing between command posts around 11:30 that night when he was hit by six rounds of friendly fire. He took four bullets in the leg, one in the hand, and one in the chest which was fortunately deflected by a cigarette case. Doohan recovered but had to have a finger on his right hand amputated. His injuries ended his army service but, undeterred, he took an Air Observation Pilot course and flew in 666 Squadron in the Royal Canadian Airforce. It was during this training that Doohan became known as "the craziest pilot in the Canadian Airforce" due to an incident which occurred early in 1945. On the Salisbury Plain in England- an RAF station was nearby- Doohan slalomed his plane down a mountainside between telegraph poles just to prove it could be done. He received an official reprimand for this stunt.
For his service in World War II, James Doohan was awarded the following decorations: Lieutenant of the Royal Canadian Order, United Kingdom 1939-1945 Star, United Kingdom France and Germany Star, United Kingdom Defense Medal 1939- 1945, United Kingdom War Medal 1939-1945, and the Canadian Volunteer Service Medal.
James Doohan died in 2005 due in part to pulmonary fibrosis which was caused by inhaling noxious substances during W.W. II.