On 27 June 1976, Wilfried Böse and Brigitte Kuhlmann, two members of the ultra-leftist Revolutionary Cells terrorist syndicate, hijack Air France Flight 139, flying from Tel Aviv to Paris, during the flight's initial stopover at Athens. Quickly thereafter, Israeli prime minister Yitzhak Rabin and defense minister Shimon Peres, both political rivals, are alerted of the hijacking.
During a refueling stop at Benghazi, Böse releases a female passenger who had seemingly suffered a miscarriage; however, unbeknownst to him, the woman had feigned it to escape. After taking off once more, the hijackers commandeer the plane to Entebbe, Uganda on 28 June, where they unite with terrorists from the Popular Front for the Liberation of Palestine; the two groups had jointly orchestrated the hijacking.
The next morning, the passengers are escorted to a dilapidated airport terminal, where they are greeted by Ugandan dictator Idi Amin, who is in league with the hijackers.Concomitantly, Rabin orders Peres and Lt. Gen. Motta Gur, the chief of staff of the Israel Defense Forces (IDF), to sketch a military operation aimed at rescuing the hostages. Peres suggests invading the airport, but Rabin and Gur reject it outright. Concurrently, the terrorists begin to segregate Israeli and non-Israeli hostages, much to Böse's fury; he compares the segregation of the hostages to the Nazi-enforced Holocaust.
Favoring a diplomatic approach, Rabin initiates negotiations with Amin, much to the detestation of Peres, who supports a military option. Rabin's diplomatic overture bears fruit – on 30 June, the hijackers release 48 non-Israeli hostages whilst retaining control over the remaining Israeli hostages. With mounting public pressure against Israel's insistence on maintaining its policy of non-negotiation with terrorists, Rabin finally concedes to initiate negotiations with the hijackers on 1 July. As a consequence, the hijackers postpone the deadline of the negotiations to 4 July. Regardless of the developments, the IDF initiates preparations for a rescue mission, consisting of the Sayeret Matkal elite commando unit, headed by Lt. Col.Yoni Netanyahu; the group soon receives support from a reluctant Rabin, who would still prefer a diplomatic solution
On 3 July, with preparations for the rescue mission codenamed Operation Thunderbolt finalized, Rabin convenes the cabinet for a vote regarding the status of the operation; they unanimously vote to proceed with the mission, with Gur's endorsement. The strike force, having already departed for Uganda, is authorized to proceed with the rescue.
That night, four Israeli C-130 Hercules transport aircraft carrying the strike force land discreetly at Entebbe. Trying to maintain the element of surprise, the unit approaches the terminal in a black Mercedes limo disguised as Amin's state vehicle. However, one of the operatives prematurely opens fire, which alerts the hijackers and the adjoining Ugandan soldiers; Böse initially fixes on killing the hostages to foil the oncoming rescue team, but changes his mind at the last second. The operatives storm the building and engage both the terrorists and Ugandan soldiers; in the ensuing melee, Netanyahu as well as Böse and Kuhlmann are killed along with the remaining terrorists and several Ugandan soldiers. With the airport secured, the strike force evacuates 102 hostages by plane.
Elsewhere, Peres congratulates Rabin on the success of the operation; the latter solemnly retorts that the preservation of peace via diplomacy is the only way to ensure the avoidance of further incidents between Israelis and Palestinians. The film's ending displays archival footage of the survivors' return to Israel, with brief notes about the fates of Rabin, Peres, Yoni Netanyahu and the lack of a peace process as of 2018.
