Mustapha finally acknowledged that St. Elmo could not be taken within that day and ordered the recall. St. Angelo's suddenly heard a burst of cheering from their brothers in St. Elmo. They had lost 200 men in the battle, in comparison to 2,000 Turks. But they knew the end was near, for there would be no more reinforcements.
St. Elmo's men readied themselves for a fight to the death. The two chaplains who had stayed with the defenders throughout the siege confessed the remaining knights and soldiers. Determined that the Mohammedans would not have the opportunity to mock or desecrate their holy relics, the knights and the chaplains hid the precious objects of the Faith beneath the stone floors of the chapel, and dragged the tapestries, pictures and wooden furniture outside and set them on fire
. They then tolled the bell of the small chapel to announce to their brethren in the nearby forts that they were ready for the end.
In the gray pre-dawn light of the 23rd of June, Piali's ships closed in for the kill. The galleys, pointing their lean bows at the ruined fort, opened up their bow chasers in unison with the first charge made by the entire Turkish army. To the astonishment of Mustapha and his council, Fort St. Elmo held for over an hour. Less than 100 men remained after that first onslaught, yet the Ottoman army was forced to draw back and re-form. The knights who were too wounded to stand placed themselves in chairs in the breach with swords in their hands.
There was something about the next attack that told the garrisons looking on from Birgu and Senglea that all was over. The white-robed troops poured down the slopes, hesitated like a curling roller above the wall, and then burst across the fort, spreading like an ocean over St. Elmo. One by one the defenders perished, some quickly and mercifully, others dying of wounds among the bodies of their friends.
The Italian Knight Francisco Lanfreducci, acting on orders received before the battle began, crossed to the wall opposite Bighi Bay and lit the signal fire. As the smoke curled up and eddied in the clear blue sky, La Valette knew that the heroic garrison and the fort they had defended to the end were lost.
It was now that Mustapha Pasha impatiently strode to view his conquest. A standard-bearer carrying the banner of Sultan Suleiman the Magnificent stepped through the breach into St. Elmo. Standing victorious on the ruins of St. Elmo's walls, with the flag of St. John in the dust at his feet, Mustapha gazed at the massive bulk of Fort St. Angelo on the horizon. “Allah!” he cried. “If so small a son has cost us so dear, what price shall we have to pay for so large a father?”
In an offensive act of cruelty, he ordered the bodies of the knights to be set apart from the common soldiers. Their heads were struck from their bodies and fixed on stakes overlooking Grand Harbor. The beheaded corpses were then stripped of their mail, nailed to crossbeams of wood in mockery of the crucifixion, and launched onto the waters of Grand Harbor that night.
It was the eve of the Feast of St. John, the patron saint of the Order. Despite the loss of St. Elmo, the Grand Master had given orders for the normal celebrations to take place. Bonfires were lit and church bells were rung throughout Birgu and Senglea. The next morning the headless bodies of the knights washed up at the base of Fort St. Angelo.
As the hours passed and no relief came, the survivors in Fort St Elmo realized that no help was going to come to them. With this bitter recognition, they resigned themselves to their fate and they started to comfort each other through these agonizing moments. They were determined to die in the service of Jesus Christ and although they were half dead from fatigue, they never rested but worked to improve their defences.
This was surely a dreadful time for our men and to make things worse, the enemy spent the whole night bombarding them, sounding the alarm and skirmishing. Clearly, they did so in order to break down the defenders so that by morning, they would be completely worn out.
As their end seemed to get closer by the hour, the last defenders of Fort St Elmo confessed to each other and implored Our Lord to have mercy on their souls for the sake of the blood that He had shed for their redemption.
On June 2nd, Admiral Dragut the legendary pirate and enemy of the Knights of St. John and all Christians in the Mediterranean arrived with his fleet at Malta. His appearance was undoubtedly a blow to the spirits of the knights who recognized the skill of their great adversary. As LaValette and Sir Oliver Starkey watched his arrival, Starkey muttered, "God help us." To which the Grand Master replied, "Yes, now the real battle begins."
Fort St. Elmo was well placed to defend the Grand Harbor from attack by sea but its low lying position at the base of the penisula left it vulnerable to attack from Mt. Scibberas as the high ground at the top of the peninsula. As the commander of Ottoman naval forces, Piali Pasha wanted to secure his fleet in the Harbor he argued that Fort St. Elmo must be captured and the first point of attack. Mustafa Pasha opposed this plan but finally relented, assuming that it would only take a few days to destroy the fort. Mustafa began moving his cannons into position for the assault and the bombardment of Fort St. Elmo began on May 24th.
Trusting the information given up under severe torture, Mustafa Pasha sent a substantial force to attack Birgu. The advance troops outpaced the main body of soldiers and were met by a number of eager young knights who sallied forth from their fort much to the chagrin of the Grand Master watching from Fort St. Angelo. He later gave orders that no troops were to leave their positions without his express command. But on this first engagement the knights were victorious and what could have been a disaster for them instead became the first defeat for Mustafa's army and the loss of several hundred of his soldiers to twelve knights of St. John. 
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