At the time of the German invasion of the Netherlands in May 1940, Smirnov and his wife lived in Napels, which since the outbreak of World War II had functioned as the terminal of the KLM route to the East Indies. He moved to Java and continued flying the route, until the Japanese invasion of the Dutch East Indies in December 1941. Though returned to military flying as a (reserve) captain in the army aviation corps, he remained also active as a civilian pilot. He evacuated Dutch women, children, and VIPs to Australia, at times taking off just minutes before the invaders arrived. Eventually, on 3 March 1942, his luck ran out. He was flying PK-AFV, a DC-3 Dakota again dubbed "Pelikaan", when he was attacked by three Japanese Zeroes. Although wounded five times in the arm, the ex-fighter pilot threw his transport into a diving spiral away from the attacking fighters to make his escape. He crashlanded the DC-3 on a sandy beach, four of his passengers dying in the event. The survivors and cargo were rescued five days later, though a packet of diamonds went missing. (For more details, see 1942 KNILM Douglas DC-3 shootdown)