The declaration of war found Konstantinos Mitsotakis at the reserve officers school of Syros, from which was placed in Macedonia, the subsequent German front. Following the collapse of the front he went to Athens and from there traveled to Crete in 1942, where he took part in the resistance against the Nazis as a leading member of the National Organization of Crete (NOC) and the National Intelligence and Sabotage Organization (NISO) which originally was the military branch of the Higher Struggle Committee of Crete (HSCC). Konstantinos Mitsotakis worked closely with allied groups (mostly British), which acted on the island against the Germans. For this activity of his, was imprisoned and sentenced twice to death, by the Germans. The first time he was pardoned on the occasion of the March 25th, 1944 National Day and was released along with other hundred or so inmates. On March 31, 1945, was exchanged for a second time, with nine comrades, with three times as many German prisoners, shortly before the surrender of the Germans in Chania. The exchange of Greek citizens with German military was unique in the history of Second World War and had to be approved by the supreme allied and German leadership. Additionally, Konstantinos Mitsotakis on the Greek side and Major Denis Ciclitiras on the side of the British, were involved in the secret delivery of the last German General, Benthag at Eleftherios Venizelos's home in Chania, early May 1945 in order to initiate the formal surrender at Heraklion, a few months later.