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Ratner was asked to lecture about his plan. Ben-Gurion seemed unenthusiastic. He asked a few questions. Golomb did not participate in the conversation but remained attentive. Ratner explained that Golomb cannot be handed all the responsibility and that a "General for Special Duties" as he called, should be appointed. Ben-Gurion turned to Golomb and asked for his opinion. Golomb delayed answering yet finally said only two words: "Ratner's right."
Thus, the path was clear to Prof. Ratner's appointment as the seventh member of the National Headquarters as Chief of the National Headquarters, who was unaffiliated with any political camp. For the first time, "Haganah" had a Chairman for its National Headquarters. Ratner filled the position for two years. In the meantime, World War II broke out and Ratner was sent on behalf of "Haganah" to assist the British Army, whose back was against the wall due to fears of a German invasion of the Middle East. Among other positions, he served in the British Headquarters in Cairo and established a special office in Haifa that gathered any possible information from Syria and Lebanon: Physical, transportation, information on sources of food and water and the possibilities for cooperation with the local population. The intention was to "get inside the heads" of the German generals, should they decide to invade the Land of Israel from the north, and make proposals for thwarting their progress through Syria to the Land of Israel in the south and to Iraq and Iran in the East.
However, a different activity of Ratner's during the first years of the war, is more memorable: He and Yitzhak Sadeh were members of the "Ratner-Sadeh Committee", which proposed an outline for the armed struggle of the Jewish Yishuv in the Land of Israel in the event, God forbid, of a German occupation. The plan proposed that after the British withdrew, all the Jewish Yishuv's people would concentrate in the fortified compound on the Carmel – which was called "Masada on the Carmel" and the "Plan of the North" – from which they would fight against the invaders and attempt to stop them until the British Army recovered and returned to the Land of Israel. Luckily, General Bernard Montgomery managed to block the progress of General Erwin Rommel's corps from Libya to Egypt, and the Land of Israel was saved. The "Ratner-Sadeh Committee" report was transferred to the "Haganah" Archive.
Serving in the "Haganah", Ratner promoted the establishment of the first General Staff (in 1939) and the appointment of Yakkov Dostrovsky (Dori) as the organization's first Chief of Staff (the terms General Staff and Chief of Staff had been coined then). After the establishment of the Palmach in 1941, Ratner had fostered and assisted it within the "Haganah". When Yitzhak Sadeh, founder of the Palmach and its first commander, gifted him with a book he wrote, he wrote him a dedication: "To Yohanan Ratner, the master of planning and improvisation".
After World War II ended, Ratner was appointed as the Head of the Planning Department of the "Haganah", alongside his regular work in the Technion, but he left it in a huff when he was not brought in on the secret of the attack on the Atlit detainee camp. After a year and a half, he returned to activity. Chief of Staff Yakov Dori, who was sent to the United Stated for procurement purposes, returned to his position and Ratner returned and joined the "Haganah" General Staff. During the first months of the War of Independence, Ben-Gurion offered Ratner the position of Acting Chief of Staff, due to the illness of the serving Chief of Staff Yakov Dori. He refused and

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