As the Germans swept east, they began the oppression and ultimately the liquidation of the Jews  in the areas they occupied.

In July, less than a month after the Germans occupied Vilna, SS Einsatzkommando 9 rounded up 6,000 Jewish men of Vilna and took them to Ponary, about 6 miles from Vilna, where they were shot. 

The next major Aktion took place beginning August 31, supposedly in retaliation for an attack against the Germans. The Germans then crowded tens of thousands of Jews from surrounding areas into Vilna.

Kovner, who was to lead the ghetto revolt, saw a woman dragged by the hair by two soldiers, a woman who was holding something in her arms. One of them directed a beam of light into her face, the other one dragged her by her hair and threw her on the pavement.

Then the infant fell out of her arms. One of the two, the one with the flashlight, I believe, took the infant, raised him into the air, grabbed him by the leg. The woman crawled on the earth, took hold of his boot and pleaded for mercy. But the soldier took the boy and hit him with his head against the wall, once, twice, smashed him against the wall.¹  

During the four day Aktion. 8,000 men and women were shot at Ponary.

Immediately following the last Aktion, the remaining Jews were herded into a small area of Vilna and walled in. Kovner related:

... when the troops herded the whole suffering, tortured, weeping mass of people into the narrow streets of the ghetto, into those seven narrow stinking streets, and locked the walls that had been built, behind them, everyone suddenly sighed with relief. They left behind them days of fear and horror; and ahead of them were deprivation, hunger and suffering - but now they felt more secure, less afraid. Almost no one believed that it would be possible to kill off all of them, all those thousands and tens of thousands, the Jews of Vilna, Kovno, Bialystok, and Warsaw - the millions, with their women and children.²

The fate of those taken to Ponary was masked by the Germans as "resettlement," but the truth got back to the ghetto. Most did not believe it was possible, but a few understood that the Germans were out to exterminate the Jews, and decided to resist.

In December 1941, activists held several meetings, where they decided to resist and to remain in the ghetto rather than trying to escape. They managed to hold a  meeting on New Year's eve. In front of the 150 Jews at 2 Straszuna Street, in a public soup kitchen, Kovner proclaimed:

Jewish youth!

Do not trust those who are trying to deceive you. Out of the eighty thousand Jews in the "Jerusalem of Lithuania" only twenty thousand are left. . . . Ponar [Ponary] is not a concentration camp. They have all been shot there. Hitler plans to destroy all the Jews of Europe, and the Jews of Lithuania have been chosen as the first in line.

We will not be led like sheep to the slaughter!

True, we are weak and defenseless, but the only reply to the murderer is revolt!

Brothers! Better to fall as free fighters than to live by the mercy of the murderers.

Arise! Arise with your last breath!³

A meeting was held three weeks later, January 21, 1942, at the home of Joseph Glazman. Representatives from the major youth groups met: Abba Kovner of Hashomer Hatzair,  Joseph Glazman of Betar,  Yitzhak Wittenberg and Chyena Borowska of the Communists and Nissan Reznik of Ha-No'ar ha-Ziyyoni

As in the Warsaw Ghetto, the groups agreed to unite. Kovner is said to have had a major part in unifying the groups.⁴ They formed the Faraynigte Partizaner Organizatzye - F.P.O. (United Partisan Organization) to prepare for mass armed resistance, perform acts of sabotage, fight with partisans, and try to ignite revolts in other ghettos. Yitzhak Wittenberg was appointed commander, and Glazman and Kovner were his staff.

Meanwhile, Kovner was writing. His poems were published by Hashomer Hatzair in Vilna, and in 1943, a smuggled poem was published for the first time in Palestine, by the newspaper Haaretz, after being smuggled out by the partisan post. It was signed Uri, Kovner's name in the underground.

In July 1943, Wittenberg, the commander of the F.P.O., was arrested at a meeting with the head of Vilna's Judenrat, Jacob Gens probably due to treachery of  Gens under Nazi threats. He was freed by other F.P.O. members, and went into hiding. The Germans threatened that if he were not released, the entire ghetto would be liquidated. 20,000 still remained alive. Pressure against the FPO was organized by the Judenrat. Wittenberg eventually gave himself up, and appointed Kovner as his successor.

A month and a half later, the Germans decided to liquidate the ghetto. The F.P.O. tried to persuade the ghetto residents not to join the deportation because they were being sent to their deaths. They proclaimed:

Jews! Defend yourselves with arms! The German and Lithuanian hangmen have arrived at the gates of the ghetto. They have come to murder us! . . . But we shall not go! We shall not stretch our necks like sheep for the slaughter! Jews! Defend yourself with arms!⁵

Most ghetto residents did not heed the proclamation.Most of these transports were being sent to labor camps in Estonia, chiefly the HKP and Kailis camps. Most of the transportees at those camps were eventually killed by the SS.

The HKP camp was commanded by Wehrmacht Major Karl Plagge, who managed to shield some of his workers from the SS. Of all the Jews of the Vilna ghetto, the 250 survivors represent the largest group of those who were transported and survived the war.

On September 1, 1943, fighting broke out between the F.P.O. and the Germans. The F.P.O. shot at the Germans, and the Germans blew up their buildings. The Germans retreated at night and allowed the Jewish police to round up the remaining ghetto residents for the transports, at the insistence of Gens, the head of the Judenrat (Jewish council).

The F.P.O. realized further resistance was pointless, as they were alone in the fight. They escaped to the forests through the sewers. They created a partisan group, destroying power and water infrastructures, freeing groups of prisoners from the Kalais labor camp, and even blew up some German military trains. Kovner wrote:

I remember the first time I blew up a train. I went out with a small group, with Rachel Markevitch as our guest. It was New Year's Eve; we were bringing the Germans a festival gift. The train appeared on the raised railway; a line of large, heavy-laden cars rolled on toward Vilna. My heart suddenly stopped beating for joy and fear. I pulled the string with all my strength, and in that moment, before the thunder of the explosion echoed through the air, and twenty-one railway cars full of troops hurtled down into the abyss, I heard Rachel cry: "For Ponar!" [Ponary]⁶

Abba Kovner survived. He organized the Beriha to Palestine.  In July 1945 he arrived at  the Jewish Brigade base in Italy, and from there traveled to Palestine to gather equipment.  While returning to Europe, he was arrested by the British and deported to Egypt, where he was  held briefly. In 1946 he joined  his wife and partner in the F.P.O., Vitka Kampner, and arrived with a few more partisans at kibbutz Ein Hahoresh. During the Israeli War of Independence.  Kovner was an officer in charge of cultural activities in the "Givati" brigade and issued a daily battle sheet.

Following the war Kovner returned to Kibbutz Ein Hahoresh and began to write. He published several collections of poems and a prose trilogy. His book of poetry Ad Lo-Or, ("Until there is no more  iight"), 1947, describes  the struggle of the  partisans in Eastern Europe. The poem, Ha-Mafteach Tzalal, ("The Key Drowned"), 1951, also about his partisan experiences is included in Mikol Ha'ahovot (1965). Preidah Me-ha-darom ("Departure from the South"), 1949,  and Admat Hahol  (Sandy ground), 1961, are additional poetry. His prose trilogy Panim el Panim ("Face to Face"), 1953, She'at Ha'efes (zero hour) and Ha-Zomet  (the junction) immortalizes the Givati brigade in the  Israeli War of Independencee,

In 1970, Kovner was awarded the Israel prize and elected Chairman of the Hebrew Writers' Association.

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