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At least 50 passengers, including children, and up to six hijackers died in the gunfight and explosion which followed the decision to send in the troops.
The crisis began two days ago after gunmen took control of the passenger jet ten minutes after take off from Athens airport.
The hijackers forced the captain to divert to Malta, where the plane landed on a remote runway of Luqa Airport, near the capital, Valletta.
The plane then sat on the runway for 24 hours while the Maltese authorities tried to negotiate the release of the hostages on board.
The hijackers released some of the hostages soon after arriving, including two wounded stewardesses and some Filipino and Egyptian women.
But shortly afterwards they brought an Israeli woman to the doorway and, without warning, shot her in the head.
A second woman was shot the following morning, and a third, also Israeli, later in the day.
Two more bodies - both killed on board the plane - were also pushed out onto the tarmac.
One of the survivors, Julie Moldes, described the scene on board the plane.
"During the gun fighting everyone hid their faces in their hands and behind seats.
"They were constantly aggressive, waving guns and shouting in everyone's faces but all the passengers kept quiet, not daring to speak or move."
Finally the Maltese Prime Minister, Carmelo Mifsud Bonnici, authorised the storming of the plane.
The commandoes began the operation by putting up a smokescreen before blowing open the luggage hold at the rear.
When they opened fire, the hijackers threw hand grenades in their direction, causing an explosion which then engulfed the plane in flames.
Eyewitnesses spoke of a loud bang preceded by a flash which lit up the sky above the Boeing 737.
The hijack has been a source of some embarrassment to the Greek authorities, who insisted that there had been five security checks on passengers boarding the jet in Athens.
Greece maintains security precautions at Athens have been stepped up since the hijack last June of a TWA airliner carrying mainly American passengers.
It later emerged that there were just three hijackers on board, two of whom died. Two crew members and 59 of the 90 passengers were killed.
Of the five people - two Americans and three Israelis - shot in cold blood while the aircraft was on the tarmac in Malta, three survived.
The surviving hijacker was named as Omar Rezaq, a Palestinian who boarded the plane under a false identity. He was linked to the extremist Abu Nidal group.
He was tried in Malta and sentenced to 25 years in jail, though he served only seven.
After his release, he went to Nigeria where the authorities handed him over to waiting FBI agents, who flew him to the United States to await trial.
In 1996 he was sentenced to life imprisonment for air piracy.
There was strong criticism of the way force was used to end the hijacking. The commandoes were accused of poor preparation and heavy-handedness.
Several of those passengers who died were killed not by the hijackers but by explosives set off by the Egyptian soldiers during the attack.
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