Napoleon's capture of Malta in June 1798 cannot be counted as one of his military triumphs. The Grand Master capitulated without offering any resistance and Napoleon made his grand entry into Valletta and within a week Von Hompesch, accompanied by a few knights, left the Island unwept, unhonoured, and unsung.

The Maltese felt that they had been let down by the Order, but before they could attempt any resistance they were talked into submission by the Bishop. Maltese that had served in the Order's army and navy were recruited into the French Republican forces, and other regiments were raised for garrison duties on the Island itself. Nobility was of course, abolished and all armorial bearings were to be removed.

After stripping the palaces, Auberges and other buildings of everything of value, Napoleon, conveniently forgetting his promises, next turned his attention to the churches; only such articles that were indispensable for the "exercise of the cult" were left while all other valuables were removed and priceless works of art in gold and silver melted down into ingots.

Nominally the Order had held the Island of Malta in fief from the King of Sicily (since 1735 this island had been amalgamated with the State of Naples and was then known as the Kingdom of the Two Sicilies), and it was to the King of the Two Sicilies that the Maltese now turned for aid and protection. At the same time deputies were despatched to seek aid from the allies of the King, the British.

A small number of British troops were landed and the French in Gozo surrendered in October l798, the Sicilian flag being hoisted on the ramparts.
As the siege wore on, the French penned in the fortifications were prevented from receiving aid because of the British blockade, while the Maltese, by this time, aided by Italian and British troops, did not have the means of assaulting the formidable bastions.

The French, having arrived at the end of their tether, were ready to capitulate but the troops of Napoleon proudly refused to submit to the Maltese rebels.

The British, on the other hand, anxious to deploy their troops and warships in other theatres of war, were eager to speed up the surrender of the French in Malta.

The Maltese had borne the brunt of the fighting and other privations, but when the capitulation was being drafted and signed neither they, nor their representatives, were allowed to participate in the negotiations.

The National Congress was dissolved and the Maltese Battalions disbanded; a Maltese regiment formed by the British, under British officers was, however, retained.