Netanyahu was killed in action on July 4, 1976, while commanding the rescue mission during Operation Entebbe.^[12] He was the only Israeli soldier killed during the raid (along with three hostages, all of the Revolutionary Cells members, all of the Popular Front for the Liberation of Palestine members, and dozens of Ugandan soldiers). The commonly accepted version of his death is that Netanyahu fired on Ugandan soldiers, and was shot in response by a Ugandan soldier from the airport's control tower. The family refused to accept this verdict and insisted instead that he was killed by the German commanding the hijackers.^[13][14] Netanyahu was shot outside the building being stormed, and would soon die in the arms of Efraim Sneh, commander of the mission's medical unit.^[15] The operation itself was a success and was renamed Mivtsa Yonatan ("Operation Jonathan" in English) in his honor.^[12]

Netanyahu was buried in Jerusalem's Military Cemetery at Mount Herzl on July 6 following a military funeral attended by enormous crowds and top-ranking officials.^[16] Shimon Peres, the then-Defense Minister, said during the eulogy that "a bullet had torn the young heart of one of Israel's finest sons, one of its most courageous warriors, one of its most promising commanders – the magnificent Yonatan Netanyahu."^[11]

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