All Jews were ordered by the occupiers to move into the Vilna Ghetto, but Kovner managed to hide with several Jewish friends in a Dominican convent headed by Polish Catholic nun Anna Borkowska in the city's suburbs.

The idea of resistance was disseminated from Vilnius by youth movement couriers, mainly women, to the ghettos from the now occupied territories of Poland, Belarus and Lithuania.

[6] Kovner, Yitzhak Wittenberg, Alexander Bogen and others formed the Fareynikte Partizaner Organizatsye (FPO), one of the first armed underground organizations in the Jewish ghettos under Nazi occupation.

[9] From September 1943 until the return of the Soviet army in July 1944, Kovner, along with his lieutenants Vitka Kempner and Rozka Korczak, commanded a partisan group called the Avengers ("Nokmim" in Hebrew) in the Rūdninkai forest near Vilnius and engaged in sabotage and guerrilla attacks against the Germans and their local collaborators.

[11][12][13] After the Soviet Red Army occupied Vilnius in July 1944, Kovner became one of the founders of the Berihah movement, helping Jews escape Eastern Europe after the war.

At the end of the war, Kovner was one of the founders of the secret organization Nakam ('Revenge'), also known as Dam Yisrael Noter ('the blood of Israel avenges', with the acronym DIN meaning 'judgement'),[14] whose purpose was to seek revenge for the Holocaust.

In pursuit of Plan A, members of the group were infiltrated into water and sewage plants in several cities, while Kovner went to Palestine in search of a suitable poison.

[17] According to Kovner's own account, Chaim Weizmann approved when he pitched Plan B and put him in touch with the scientist Ernst Bergmann, who gave the job of preparing poison to Ephraim Katzir (later president of Israel) and his brother Aharon.

[16][17] In April 1946, members of Nakam broke into a bakery used to supply bread for the Langwasser internment camp near Nuremberg, where many German POWs were being held.

[21] However, the tone of the pages, which called for revenge for the Holocaust and referred to the Egyptian enemy as vipers and dogs, upset many Israeli political and military leaders.

"[24] His first battle page, entitled "Failure", started a controversy that still continues today when it accused the Nitzanim garrison of cowardice for surrendering to an overwhelming Egyptian force.

[29] Kovner's book of poetry עד-לא-אור ("Ad Lo-Or", English: Until No-Light), 1947, describes in lyric-dramatic narrative the struggle of the Resistance partisans in the swamps and forests of Eastern Europe.