While Nelson was gathering his fleet and searching for the French, Bonaparte had secured the first stage of his plan for the invasion of Egypt.
Arriving off Malta on 9 June, he demanded that the island's ruler, Ferdinand von Hompesch zu Bolheim, the Grand Master of the Knights Hospitaller (or Knights of St. John of Jerusalem) to allow his fleet to enter the harbour and purchase provisions.
 Hompesch refused, insisting that only two ships at a time could enter the port.
Bonaparte responded by opening fire on the harbour defences and on 11 June landed soldiers at seven sites around Malta under General Louis Baraguey d'Hilliers.
Coming under fire from the 2,000 native Maltese soldiers that mustered against the invasion, skirmishing continued in the western part of the island for 24 hours, until General Claude-Henri Belgrand de Vaubois entered Mdina and the defenders withdrew to the fortress of Valletta.
The Maltese troops refused to continue the fight without support from their government, and negotiations followed in which Hompesch and the knights agreed to abandon Malta on condition of financial compensation amounting to 3 million Francs.
In exchange, Bonaparte gained the entire Maltese archipelago, including fortresses, military stores and cannon, the small Maltese Navy and Army and the entire property of the Roman Catholic Church in Malta.

The Maltese position had already been severely weakened by the large number of Frenchmen who were part of the Order, who refused en masse to take up arms against Bonaparte.
The French Revolution had already significantly reduced the Knights' income and their ability to put up serious resistance to Bonaparte was seriously compromised by a lack of resources.
On 12 June, Bonaparte finally announced to his troops the destination of the expedition and on 19 June he sailed for Alexandria, initially steering east towards Crete.
He left behind Vaubois and 4,000 men to maintain Malta as a base to control the Central Mediterranean.
To ensure that news of the impending attack on Egypt did not spread ahead of the fleet, Brueys ordered that any merchant ships that sighted the convoy during the passage were to be seized and detained until his force had reached Alexandria.
On 26 June, the British gained the first firm intelligence of French intentions, when the frigate HMS Seahorse under Captain Edward Foote encountered and captured the French frigate Sensible, which was returning to Toulon from Malta with a cargo of treasure and wounded soldiers, including General d'Hilliers.
From these prisoners the destination of the French fleet was discovered and Seahorse, joined shortly afterwards by Terpsichore, sailed in pursuit, hoping to encounter Nelson.
While Nelson was gathering his fleet and searching for the French, Bonaparte had secured the first stage of his plan for the invasion of Egypt. Arriving off Malta on 9 June, he demanded that the island's ruler, Ferdinand von Hompesch zu Bolheim, the Grand Master of the Knights Hospitaller (or Knights of St. John of Jerusalem) to allow his fleet to enter the harbour and purchase provisions.  Hompesch refused, insisting that only two ships at a time could enter the port. Bonaparte responded by opening fire on the harbour defences and on 11 June landed soldiers at seven sites around Malta under General Louis Baraguey d'Hilliers. Coming under fire from the 2,000 native Maltese soldiers that mustered against the invasion, skirmishing continued in the western part of the island for 24 hours, until General Claude-Henri Belgrand de Vaubois entered Mdina and the defenders withdrew to the fortress of Valletta. The Maltese troops refused to continue the fight without support from their government, and negotiations followed in which Hompesch and the knights agreed to abandon Malta on condition of financial compensation amounting to 3 million Francs. In exchange, Bonaparte gained the entire Maltese archipelago, including fortresses, military stores and cannon, the small Maltese Navy and Army and the entire property of the Roman Catholic Church in Malta.
The Maltese position had already been severely weakened by the large number of Frenchmen who were part of the Order, who refused en masse to take up arms against Bonaparte. The French Revolution had already significantly reduced the Knights' income and their ability to put up serious resistance to Bonaparte was seriously compromised by a lack of resources. On 12 June, Bonaparte finally announced to his troops the destination of the expedition and on 19 June he sailed for Alexandria, initially steering east towards Crete. He left behind Vaubois and 4,000 men to maintain Malta as a base to control the Central Mediterranean. To ensure that news of the impending attack on Egypt did not spread ahead of the fleet, Brueys ordered that any merchant ships that sighted the convoy during the passage were to be seized and detained until his force had reached Alexandria. On 26 June, the British gained the first firm intelligence of French intentions, when the frigate HMS Seahorse under Captain Edward Foote encountered and captured the French frigate Sensible, which was returning to Toulon from Malta with a cargo of treasure and wounded soldiers, including General d'Hilliers. From these prisoners the destination of the French fleet was discovered and Seahorse, joined shortly afterwards by Terpsichore, sailed in pursuit, hoping to encounter Nelson.
Mediterranean campaign of 1798