In the exchange of fire the fuselage was punctured, causing a rapid depressurization. The aircraft was forced to descend to 14,000 feet (4,300 m) to allow the crew and passengers to breathe.

Libya was the original destination for the terrorists, but due to the negative publicity the hijacking would have had if flown to Libya and the fact that the plane did not have enough fuel, Malta was chosen as a more suitable option.

The aircraft was now running dangerously low on fuel, experiencing serious pressurization problems and carrying a number of wounded passengers.

Maltese authorities still did not give permission for the aircraft to land.

The EgyptAir 648 terrorists insisted, and they forced the pilot, Hani Galal, to land at Luqa Airport.

As a last-ditch attempt to stop the landing, the runway lights were switched off, but the pilot still managed to land the damaged aircraft safely.
On the ground in Malta, the hijackers demanded fuel. When they did not get it, they shot two American and three Israeli passengers in the back of the head, three of whom miraculously survived.

After hours of negotiations, Egyptian commandos stormed the aircraft by using an explosive device that killed many passengers.

The commandos boarded the aircraft and fought with the hijackers, who threw several hand grenades inside the cabin.