In June 1941, Nazi Germany invaded the Soviet Union and soon captured Vilnius. A ghetto was established in the city and Jews captured for labor were taken by force to the Ponary massacre. Iser and his brother Yitzhak fled the ghetto just before one of those actions but returned to it later. Lubotzky joined the United Partisan Organization (Fareynikte Partizaner Organizatsye; FPO), the secret underground that was set up in the ghetto and fought against the Germans. At the decision of his underground commanders, he was recruited to the ghetto's secret-police unit to gather intelligence. Josef Glazman, one of the leaders of United Partisan Organization, informed him of the underground's goals and shared with him various secret plans. After his release, he continued his activities in the underground. On the day of the liquidation of Vilna's ghetto in September 1943, a small-scale revolt broke out and Lubotzky left the ghetto with a group of about 100 partisans under Abba Kovner, escaping through the sewers to join partisans operating in the surrounding forests.