When the Nazi Germans entered Lithuania, in 1941, at the start of Operation Barbarossa, he formed a military unit of roughly 600 members, which was not subordinate to the Lithuanian Activist Front or the Provisional Government of Lithuania, and engaged in firefights with the Soviet army for the control of Kaunas. On the evening of June 23, most of the city was in the hands of the insurgents. On the night of 25–26 June, a pogrom led by Klimaitis unit was instigated by Nazi Security Police (Sipo) and SD (Sicherheitsdienst or Security Service, the intelligence arm of the Nazi Party), under SS Brigadeführer Franz Walter Stahlecker. By 28 June 1941, according to Stahlecker, the commander of the German Einsatzgruppe A, 3,800 people had been killed in Kaunas and a further 1,200 in surrounding towns in the region. Klimaitis' men destroyed several synagogues and about sixty Jewish houses. Some sources claim that the number of victims in Stahlecker's report were probably exaggerated.. After the war, Algirdas Klimaitis, moved to Hamburg, Germany, where he died in 1988.