Nazis transported the Jews by train mostly.
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The Nazis believed many, often contradictory, things about the Jews. One of the Nazis' favourite themes was that the Jews and the Germans were locked in some mysterious struggle for domination of Germany, Europe, even the world!
the Nazis would kill them
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This question is odd. It is formulated in a way that suggests there was an actual war between 'the Jews' and the Nazis. There was the Holocaust, in which the Nazis murdered about 6 million harmless and defenceless Jews. That began in late 1941/early 1942. The idea that there was an actual war between Jews and Nazis is false.
Primarily Jews, but other minorities were targeted by the Nazis.