On 18 February 1800 lookouts on the British ship HMS Alexander sighted the French and gave chase, followed by the rest of Nelson's squadron while Keith remained off Valletta.

Although most of the French ships outdistanced the British pursuit, one transport was overhauled and forced to surrender, while Perrée's flagship Généreux was intercepted by the much smaller frigate HMS Success.

The French fleet, under the command of Vice-Admiral François-Paul Brueys D'Aigalliers was directed to anchor in Aboukir Bay, 20 mi (32 km) northeast of Alexandria and support the army ashore.

During an auction of church property on 2 September 1798, an armed uprising had begun that had forced the French garrison, commanded by General Claude-Henri Belgrand de Vaubois, to retreat into the capital Valletta by the end of the month.

[6] The garrison, which numbered approximately 3,000 men, had limited food stocks, and efforts to bring supplies in by sea were restricted by a squadron of British and Portuguese ships stationed off the harbour.

[10] In January 1800, recognising that Valletta was in danger of surrendering if it could not be resupplied, the French Navy prepared a convoy at Toulon, consisting of Généreux, under Captain Cyprien Renaudin,[11] the 20-gun corvettes Badine and Fauvette, and the 16-gun Sans Pareille, and two or three transport ships.

[9] The force was under the command of Contre-amiral Jean-Baptiste Perrée, recently exchanged under parole after being captured off Acre the previous year, and was instructed to approach Valletta along the Maltese coast from the southwest with the intention of passing between the blockade squadron and the shore and entering Malta before the British could discover and intercept them.

[12] While the French planned their reinforcement, the Royal Navy was preparing to replace the 500 Portuguese marines stationed on Malta with 1,200 Neapolitan troops supplied by King Ferdinand.

[16] At daylight on 18 February, lookouts on Alexander sighted the French convoy sailing along the Maltese coast towards Valletta and gave chase, with Nelson's three ships visible to seawards.

At 08:00 the transport Ville de Marseille was overhauled, and surrendered to Lieutenant Harrington's ship, but the other smaller vessels hauled up at 13:30 and made out to sea, led by Badine.

Remaining on deck, he called to his crew "Ce n'est rien, mes amis, continuons notre besogne" ("It is nothing, my friends, continue with your work") and gave orders for the ship to be turned, when a cannonball from the second broadside from Success tore his right leg off at the thigh.

[10] The presence of the British squadron off Malta at the time of the arrival of the French convoy was largely due to luck, a factor that Ball attributed to Nelson in a letter written to Emma Hamilton shortly after the battle: "We may truly call him a heaven-born Admiral, upon whom fortune smiles wherever he goes.

"Although pleased with the result of the engagement, Lord Keith issued strict instructions that Nelson was to remain in active command of the blockade and on no account to return to Palermo.

In March, while Nelson was absent at Palermo, the ship of the line Guillaume Tell, the last survivor of the Nile, attempted to break out of Malta but was chased down and defeated by a British squadron led by Berry in Foudroyant.