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After the military takeover of Estonia, the USSR in June 1940 demanded a shadow government to be set up that subsequently dissolved Estonia's civil society, sovietized its government institutions, nationalized the economy and shut down free press and civic organizations. In an atmosphere of terror and massive human rights violations, a puppet parliament was elected in July 1940. On 21. July, it proclaimed the Estonian Soviet Socialist Republic which was incorporated into the Soviet Union on 6. August 1940. Leading countries of the free world did not recognize the move and continued to recognize the Republic of Estonia and its diplomatic representatives throughout the era of occupation.
Imposition of a Communist terror regime shattered the existing way of life. Hundreds of historical monuments were wiped out and more than a million banned books were destroyed during the first year of occupation alone. From June 1940 to August 1941, more than 7000 persons were arrested and about 200 shot. Almost all leading politicians, including former Prime Ministers and cabinet members, were arrested and executed or sent to die in Siberian prison camps. Communist crimes reached genocidal proportions on 14. June 1941 when more than 10.000 persons with families were deported to Soviet Union's remote Siberian regions. About a third of the deportees were men, who were separated from families in assembly stations and sent to prison camps where most perished from cold, hunger and forced labor. Women and children, the majority of deportees, were transported in inhumane conditions to Kirov and Novosibirsk oblasts where many did not survive. A second wave of deportation was launched in July 1941, but was limited to Estonia's islands as invading German forces closed in.
In violation of international law, a forced mobilization into the Red Army was ordered by the Soviet Union after war broke out between it and Nazi Germany and as many as 36.972 Estonian men were transported to Russia. Thousands of civilians were also involuntarily evacuated to the Soviet rear. During the first year, at least 10.440 of the mobilized died from hunger and diseases in labor camps or repressions by the Soviet People's Commissariat of Internal Affairs. Between 9700 and 20.000 forcibly mobilized Estonian citizens were killed in the battles of World War II. A fresh wave of terror hit Estonia after war broke out between Soviet Union and Nazi Germany.
At least 2446 civilians were executed without trial by death squads, special military and Soviet regular forces, with many being tortured to death.
To put down local resistance, villages and whole towns were burnt to the ground. Largest mass murders were committed in Tartu, Kuressaare, Eerikvere and Kautla.
In all, the Soviet regime repressed at least 52.750 Estonian inhabitants during 1940-41 and 18.090 lost their lives. During 1941-44, at least 2409 persons were killed in Estonia by Soviet air bombardment. The air raids of March 1944 completely destroyed the border town of Narva and caused extensive damage in Tallinn, where 750 civilians died. Thousands of Estonians fought in German forces or Finnish volunteer units and died in battle as the Red Army advanced into Estonia.