On 9 June 1798 the fleet of the Egyptian expedition — nearly four hundred sail — appeared off Valletta and asked to take on water. Grand Master Ferdinand von Hompesch limited access to four ships at a time; that was the pretext awaited. Landings began on the 10th at several points on the island.
The place was among the most fortified in Europe, but the order no longer had the means to defend it: the French knights, about half the strength, refused to fire on their compatriots, and the Maltese population no longer supported a bankrupt religious aristocracy. Hompesch capitulated on 12 June and abdicated. It was the end of a sovereign state more than two and a half centuries old.
Bonaparte stayed six days and governed as though he had six years. He abolished slavery and freed the galley captives, suppressed the Inquisition and noble titles, created primary schools and a university, reorganised finances and hospitals. He also had the order's treasure seized and loaded aboard L'Orient — which would explode at Aboukir seven weeks later with part of the spoils.
The garrison left under Vaubois found itself isolated after the fleet's destruction. The Maltese rose in September 1798, the British blockaded the island, and the garrison capitulated in September 1800. Malta stayed English; London's refusal to evacuate it, contrary to the treaty, would be the immediate cause of the renewed war in May 1803.