Claude-Henri Belgrand de Vaubois

Still, on 18 September, a Portuguese squadron of four ships began a blockade of Malta. That blockade - although varying in the number and national composition of the ships - continued until the French surrendered. Nelson dispatched British forces under the command of Captain Alexander Ball, who arrived on 12 October 1798. The Maltese insurrectionist forces forced the French to withdraw to Valletta and the Three Cities around the Grand Harbour. On 28 October Gozo Island fell as the French commander there surrendered himself and his 217 men to Captain Ball. With General Vaubois's forces besieged in Valletta, Captain Ball's ships continued the blockade. Expecting the imminent French capitulation, Nelson wrote to Ball in January 1799:

... Respecting the situation of Malta with the King of Naples, it is this – he is the legitimate Sovereign of the Island: therefore, I am of opinion his Flag should fly. At the same time, a Neapolitan garrison would betray it to the first man who would bribe him. I am sure the King would have no difficulty in giving his Sovereignty to England; and I have lately, with Sir William Hamilton, got a Note that Malta should never be given to any Power without the consent of England ...

P.S. – In case of the Surrender of Malta, I beg you will not do anything which can hurt the feelings of their Majesties. Unite their Flag with England’s, if it cannot, from the disposition of the Islanders, fly alone.

In February 1799, the Maltese insurgents, having lost hope in an intervention of King Ferdinand, requested that Ball, who had previously landed near the village of Qrendi on the south of the island, preside over the National Assembly. He changed the name of the assembly to that of National Congress and declared himself chief of government. In March, the Congress appealed to King George III to assume sovereignty over Malta, but no answer came from Pitt’s ministry.

The starving French garrison received a little relief at the beginning of February 1799. The frigate La Boudeuse ran the blockade and entered the Grand Harbour. However, she was the last ship to re-supply Vaubois and his men.

On 1 November 1799 Nelson was off Valletta on board the Foudroyant. Vaubois, who was still hoping for relief from France, summarily rejected a new surrender demand. Vaubois wrote: "Mindful of being worthy of the respect of your country, as you are with our own, we are resolved to defend this fortress to the last."

Nelson ordered Ball to take command of the Maltese forces – about 2,000 Maltese troops along with about 1,500 irregulars, unpaid, ill-equipped and half-starving. A hard pressed King Ferdinand agreed to confirm Ball as Governor of Malta.

The whole Maltese population, running short of essential provisions, was living close to famine so that the siege was turning into a race of which side would starve first. The British and Maltese, together with a Neapolitan contingent of 1,200 men, got some relief in January 1800.

However, General Vaubois waited in vain for supplies. French preparations had dragged on until Napoleon—now Premier Consul—appointed Contre-amiral Jean-Baptiste Perrée to command a relief expedition. The squadron, comprising Le Généreux (one of the two survivors of the Battle of the Nile), three corvettes serving as armed storeships, and one armed storeship, all with some 3,000 men, arms, food and ammunition on board, sailed from Toulon-sur-Mer on 6 February 1800. The expedition ended in disaster. On the morning of 18 February English ships met the French squadron off Lampedusa island. Contre-amiral Perrée was killed at the start of the action and at 1.30 p.m. Le Généreux struck her colours. The rest of the French convoy returned to Toulon.

On 24 August Vaubois dispatched the frigates La Diane and La Justice to run the blockade to France. The Success sighted them, with the Northumberland and the captured Le Généreux, now crewed by the British, giving chase. The British captured La Diane but La Justice escaped under cover of darkness.

The siege was nearing its end. The French garrison had eaten all the horses, the mules, the dogs, the cats and the rats of Valletta. Finally, on 4 September 1800, Vaubois sent an emissary under a flag of truce to the British commander Major-General Henry Pigot. The following day, Pigot and Captain George Martin, RN, negotiated terms of surrender with General Vaubois and Contre-amiral Villeneuve. (Ironically the French excluded Captain Alexander Ball, as chief of the Maltese, from the negotiations, as the French did not want to surrender to the Maltese.) The British granted Vaubois and the French fair terms and the honours of war, including the right to keep their arms and spoils. Vaubois and his troops were quickly repatriated to Marseilles.