His unit was incorporated in the Soviet army after the Soviet occupation of Lithuania. During Operation Barbarossa the unit was dislocated near the Narach lake in Belarus. It was ordered to scout ahead, but Morkūnas and his men deserted back to Lithuania, as they were hopeful that the German army could still liberate Lithuania. After giving away his units' horses in a nearby village, they set off and were met by the Germans, who let the men return to their country. Morkūnas participated in the 1941 June uprising. Morkūnas spent the time of German occupation of Lithuania in his home village of Zbaras working at his parents farm. In 1944, when Germany was retreating, Morkūnas organized the anti-Soviet resistance around Šiluva.
