'Flags Over Berlin' is the story of one of the most important intelligence missions of the World War II - Operation 'Alsos'. Sir Winston Churchill sends his most trusted aid - a British Wing Commander Mark Spencer - to the besieged Berlin in late April 1945 under the guise of a newspaper correspondent attached to the frontline units of the Red Army preparing to storm the city. The real task, however, is to retrieve whatever documents are left behind by Nazi nuclear scientists. In doing so Mark becomes a witness of a heroic feat performed by his newfound friends from the Soviet Allies camp - lieutenant Rahim Koshkarbayev and private Grisha Bulatov - the first of many heroes to place a Flag of Victory over the German Reichstag. An unlikely encounter with a German Helferinen squad member Isabel leaves Mark wondering if Hitler might have escaped justice with assistance of SS-Obersturmbahnführer Otto Skorzeny.