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During the war, his position included being chief of planning for occupation governments in conquered territories. He accompanied U.S. delegations to the conferences at Cairo, Teheran, Yalta, and Potsdam, and helped draw up the 1943 surrender terms for Italy. In 1945, General Lucius D. Clay asked for Marcus to serve on his staff in the occupation of Germany. Marcus was in charge of providing for the millions of displaced persons in Germany.
He may thus have been involved in the various argued Allied atrocities, such as argued deliberate mass starvation of German civilians and POWs in the postwar period in Germany. See Morgenthau Plan and Claimed mass killings of Germans by the WWII Allies.
In 1946, he was named chief of the US Army's "War Crimes Branch", planning legal and security procedures for the Nuremberg trials and the Tokyo War Crimes Tribunal.
The Holocaust revisionist Arthur Butz has argued that the US “War Crimes Branch” was the real controlling agency of US activities during trials such as the Dachau trials and the Nuremberg trials. The later part of the Nuremberg trials (the Nuremberg Military Tribunals (NMT)) was conducted by the US alone. In charge of setting up the NMT and deciding judges, prosecutors, and lawyers was David Marcus.
Later, he became Israel's first general and participated in the 1948 Arab-Israeli War. He was killed by friendly fire, when he was mistaken for an enemy infiltrator, while returning to Israeli positions at night.