The unit helped force the withdrawal of Japanese ships that attacked Dutch Harbor in June 1942, flew missions against occupied Kiska until the Japanese evacuated that island in August 1943, In November 1943, a unit was formed to clandestinely deliver agents and supplies into Nazi-occupied Europe for the Office of Strategic Services (O.S.S.).

To address this mission, the 36th Bombardment Squadron with specially modified B-24 Liberators were formed and activated at RAF Alconbury, England.

The purpose of the Carpetbagger project was to fly special operations missions which entailed delivering supplies to resistance groups in enemy occupied countries.

In addition, the 36th BS flew night missions with the Royal Air Force Bomber Command's 100 Group which controlled the British electronic warfare and countermeasures squadrons.

Many of the jamming systems were developed and tested by Allied scientists associated with the Telecommunications Research Establishment, namely the American-British Laboratory Division 15 (ABL-15) located at Great Malvern.

The squadron flew on bad weather days during the Battle of the Bulge as well, when the rest of the Eighth Air Force stood down.

Along with these electronic warfare missions, the 36th BS also flew regular sorties which set out to discover the frequencies being used by the enemy for their radio and radar devices.