[13] Several days before the war began, USS Liberty was ordered to proceed to the eastern Mediterranean area to perform a signals intelligence collection mission in international waters near the north coast of Sinai, Egypt.

The following day, Admiral Martin replied: "Liberty is a clearly marked United States ship in international waters, not a participant in the conflict and not a reasonable subject for attack by any nation.

The Navy said a large volume of unrelated high-precedence traffic, including intelligence intercepts related to the conflict, were being handled at the time; and that this combined with a shortage of qualified radiomen contributed to the delayed transmission of the withdrawal message.

[23]: 111 ff Official testimony combined with Liberty's deck log establish that throughout the morning of the attack, 8 June, the ship was overflown, at various times and locations, by IAF aircraft.

At about 05:45 Sinai time, a ship-sighting report was received at Israeli Central Coastal Command (CCC) in respect of Liberty, identified by an aerial naval observer as "apparently a destroyer, sailing 70 miles [110 km] west of Gaza".

[27] About the same time, an Israeli jet fighter pilot reported that a ship 20 miles (32 km) north of Arish had fired at his aircraft after he tried to identify the vessel.

Rabin reiterated the standing order to sink any unidentified ships in the area, but advised caution, as Soviet vessels were reportedly operating nearby.

[32] Moreover, Israeli forces had standing orders to fire on any unknown vessels sailing in the area at over 20 knots (37 km/h; 23 mph), a speed which, at the time, could be attained only by warships.

Rabin ordered the torpedo boats to remain at a safe distance from the ship, and sent in two Aérospatiale SA 321 Super Frelon helicopters to search for survivors.

During the early part of the air attack and before the torpedo boats were sighted, Liberty sent a distress message that was received by Sixth Fleet aircraft carrier USS Saratoga.

McGonagle testified at the naval court of inquiry that during the latter moments of the air attack, it was noted that three high speed boats were approaching the ship from the northeast on a relative bearing of approximately 135 [degrees] at a distance of about 15 [nautical] miles.

[citation needed] Oren recalled receiving a similar response from the Ibrahim el Awal, an Egyptian destroyer captured by Israel during the Suez Crisis, and was convinced that he was facing an enemy ship.

[23]: 39  Lucas, who had left the command bridge during the air attack and returned to assist McGonagle,[23]: 14  believed that the sound of gunfire was likely from ammunition cooking off, due to a nearby fire.

[48] At 12:35Z (14:35 local time)[47] one torpedo hit Liberty on the starboard side forward of the superstructure, creating a 39 ft (12 m) wide hole in what had been a cargo hold converted to the ship's research spaces and killing 25 servicemen, almost all of them from the intelligence section, and wounding dozens.

According to transcripts of intercepted radio communications, published by the U.S. National Security Agency, at about 14:30, near the beginning of the torpedo boat attack, two IAF helicopters were dispatched to Liberty's location.

A communication to the Israeli ambassador on 10 June, by Secretary Rusk stated, among other things: At the time of the attack, the USS Liberty was flying the American flag and its identification was clearly indicated in large white letters and numerals on its hull.

The subsequent attack by the torpedo boats, substantially after the vessel was or should have been identified by Israeli military forces, manifests the same reckless disregard for human life.

[52][53]George Lenczowski notes: "It was significant that, in contrast to his secretary of state, President Johnson fully accepted the Israeli version of the tragic incident."

He notes that Johnson himself included only one small paragraph about the Liberty in his autobiography,[54] in which he accepted the Israeli explanation, minimized the affair and distorted the number of dead and wounded, by lowering them from 34 to 10 and 171 to 100, respectively.

According to an Israel Foreign Ministry letter to the Israeli Embassy in Washington: In the grave situation that has been created, the only way to soften the result is for us to be able to announce to the U.S. government already today that we intend to prosecute people for this disaster.

As a common root of these problems, Israel blamed the combination of alarm and fatigue experienced by the Israeli forces at that point of the war when pilots were severely overworked.

[82] Meadors states that the classification of the attack as deliberate is the official policy of the USS Liberty Veterans Association,[83] to which survivors and other former crew members belong.

Citing Ennes's book, Lenczowski notes: Liberty's personnel received firm orders not to say anything to anybody about the attack, and the naval inquiry was conducted in such a way as to earn it the name of "coverup".

[94] Lenczowski notes that while the Israeli decision to "attack and destroy" the ship "may appear puzzling", the explanation seems to be found in Liberty's nature and its task to monitor communications from both sides in the war zone.

[96] The 1981 book Weapons by Russell Warren Howe says that Liberty was accompanied by the Polaris ballistic missile-armed Lafayette-class submarine USS Andrew Jackson, which filmed the entire episode through its periscope but was unable to provide assistance.

[103] Admiral Thomas H. Moorer, former Chairman of the Joint Chiefs of Staff and a critic of the official U.S. government version of events, chaired a non-governmental investigation into the attack on the Liberty in 2003.

Within an hour of learning that the Liberty had been torpedoed, the director of the NSA, LTG Marshall S. Carter, sent a message to all intercept sites requesting a search of communications that might be connected to the attack or any reaction to it.

[106] These revelations were elicited as part of a Freedom of Information Act lawsuit by Florida bankruptcy judge and retired naval aviator Jay Cristol.

"[106] On 2 October 2007, The Chicago Tribune published a special report[7] into the attack, containing numerous previously unreported quotes from former military personnel with first-hand knowledge of the incident.

[115] The documentary argues that Israel knew the ship was American, and planned to blame its sinking on Egypt in order to draw the United States into the war on the Israeli side.