Complex sentence: Military counterintelligence of the Red Army and later of the Soviet Army, throughout all its history was controlled by the Soviet secret police (Cheka, GPU, NKVD,...) departments (names vary over the time).
Split into simpler sentences: Military counterintelligence of the Armed Forces of the Union of Soviet Socialist Republics, throughout all its history was controlled by the nonmilitary structure. Part of Soviet secret police (Cheka, GPU, NKVD,...) departments (names vary over the time).