Nathan was deported from Westerbork alongside his daughter, Betty, and wife, Rebecca Diamant, in September 1942.
Nathan was deported during the Cosel period, and thus the SS removed him from the train in Silesia. The train, with Rebecca and Betty onboard, continued onward to Auschwitz where they were both gassed upon arrival.
Nathan spent time at various labor camps in Silesia before showing up on a transport dated 10 Feb 1945 from Buchenwald to Groß-Rosen. It is unclear when he arrived at Buchenwald (there is no entry date on his file), but he was presumably liberated at Groß-Rosen at the end of the war.