War returned in the late summer of 1939 and Classen was briefly arrested in 1940. This turned out to be the first of several periods of detention during the war years. After this she worked clandestinely with the . She also secretly housed the resistance fighter Ilse Stillmann and the deserter/resistance fighter (and talented document forger) Oskar Huth. After the failure of the plot of July 1944 to assassinate the nation's leader, Gertrud Classen was able to provide forged papers for (who had been involved in the plot) and to help him disappear, which he did successfully till after the war was over. In Autumn 1944 she was also involved in producing forged food stamps which meant that Ilse Stillmann was not merely kept hidden from the authorities, but fed.