In 1940 Lithuania fell under Soviet-rule and everywhere in Lithuania  there were groups of resistance to be found,  fighting against the Soviets.  In Pakruojis and surroundings the Pakruojis Squad was founded,  organised and  headed  by Antanas Gasciunas and Zukauskas. About a hundred men took part in this squad. The name of the squad was Saulys .

In June 1941, about ten days before the German invasion, two Jewish families from Pakruojis, namely Kolitzman and Kaplan were forced by the Soviets to leave Pakruojis for Siberia. In this way they would survive (which they never should have imagined at that time). Actually they live in Israel now.

In early July 1941, when the Germans occupied  Lithuania  and had driven back the Soviets, the activities of these squad continued to exist for several months.  Afterwards the active squad members enlisted in police- and self-defense units.  The Germans appointed the lawyer Petras Pozela as the chief of the Pakruojis Squad.  The Germans, Petras Pozela and his men together with the squad  of Linkuva, a town near Pakruojis, were responsible for the atrocious killings of the Jewish men, women and children of Pakruojis in 1941;  the men (appr.100), accompanied by their rabbi were shot by the Germans in July 1941 and the  women and children ( appr. 200) were shot by the Pakruojis and the Linkuva Squad (the white arm-banders) in August 1941, all at Morkakalnis, about 2 km. from Pakruojis.

The Jewish community of Pakruojis didn't exist anymore.