Action of 31 March 1800 fleet anchored in Aboukir Bay to support the troops ashore and was surprised and almost completely destroyed on 1 August by a British fleet under Rear-Admiral Sir Horatio Nelson. Only two ships of the line and two frigates escaped the Battle of the Nile from the 17 French ships that participated in the action. Of the survivors, the ship of the line "Généreux" sailed for Corfu while "Guillaume Tell", under Contre-amiral Pierre-Charles Villeneuve, reached Malta with the two frigates. When Villeneuve arrived at Malta in September 1798, the island was already in turmoil: the dissolution of the Roman Catholic Church
Sir Thomas Thompson, 1st Baronet to allow them to withdraw. Thompson himself was wounded in the battle. Thompson was later given command of a squadron, and carried out cruises in the Mediterranean, intercepting French and Spanish ships. He returned to Gibraltar, but was ordered to sea again in June 1798 to reinforce Nelson's squadron in their hunt for the French fleet that had earlier escaped from Toulon. He was with Nelson when they located the French fleet, under the command of Vice-Admiral Brueys, moored in Aboukir Bay. In the ensuing engagement Thompson came to the assistance of , which had run aground on shoals in