The cruelties of first Soviet occupation, of a scale not seen in Lithuania since the Russian Empire rule, led to a widespread despise of the regime in less than a year. For example in four days between June 14 and June 18 of 1941 alone some 40 000 people from educated families were exiled to Siberia and Soviet labor camps (almost half of them 16-year-old or younger, 556 infants under 1 year, families typically separated), most never to return alive. Others were arrested with many later tortured and massacred in places like Rainiai and Cherven.
When the German Reich declared war on the Soviet Union the Lithuanians staged a June Revolt and managed to liberate most of the country. However, the German armies came in and while Germany did not immediately abolish the provisional government (possibly hoping for similar anti-Soviet revolts elsewhere) they rendered it powerless. By August all forms of self-rule were extinguished; by November all Lithuanian political parties banned.
The new Nazi German occupation brought a relief from the Soviet persecutions but it had its own target: the Jews. Some of them have fled Europe (never to return), most of the rest were killed (often after a brief life in forced ghetto or a deportation to a concentration camp in German-ruled lands elsewhere). The number of Jews living in Lithuania declined by ~88% by the time of 1959 census.
By 1944 the Germans were losing the war and the Soviets occupied Lithuania yet again. Knowing what to expect some 100 000 Lithuanians fled Lithuania beforehand. Two Soviet occupations led to a far greater loss of life than the Nazi German occupation, leading to a popular opinion that World War 2 ended for Lithuania only in 1990. Lithuania lost ~8% of its pre-WW2 inhabitants due to Nazi actions and ~32% due to Soviet actions (until the year 1953), some 40% in total (1,15 million out of 3 million). 1/3 to 1/2 of this number were killed. Well over 90% of victims were civilians.