Kammala jumla mai zuwa: USSR ta kafa tsarin zalunci; yawancin manyan jami'an farar hula da na soja, masu ilimi da masana'antu an kama su, kuma galibi an kashe su jim kaɗan bayan haka. Soviet repressions ya ƙare a ranar 14 ga Yuni 1941 tare da
da yawaitar mutane 11,000 zuwa Siberia, daga cikinsu fiye da rabin sun mutu a cikin yanayin rashin mutuntaka. Lokacin da Jamusanci Operation Barbarossa tare da rakiyar sojojin guerrilla na Estonia da ake kira "Brothersan uwan daji" suka fara adawa da Tarayyar Soviet a ranar 22 ga Yuni 1941 a cikin abin da ake kira "Yakin bazara" (), kimanin samari 34,000 na Estonia an tilasta su shiga cikin Red Army, ƙasa da kashi 30% daga cikinsu sun tsira daga yaƙin. Sojojin Soviet sun fara aiwatar da manufofin ƙone ƙasa. NKVD ta kashe fursunonin siyasa da ba za a iya kwashe su ba. Mutanen Estonia da yawa sun shiga cikin daji, suka soma yaƙin neman zaɓe da ake yi a ƙasar. A watan Yuli, Wehrmacht na Jamus ya kai kudancin Estonia. Tarayyar Soviet ta kwashe Tallinn a ƙarshen watan Agusta tare da asara mai yawa, kuma sojojin Jamus sun kammala kama tsibiran Estonia a watan Oktoba.