He fought in the campaigns undertaken by Admiral Truguet's fleet - the bombardment of Oneglia, the Naples operation led by Latouche-Tréville, and finally the attack on Cagliari on Sardinia.

Bonaparte noted Brueys's conduct in Italy and made him commander-in-chief of the fleet that would transport his army for the Egyptian campaign, with the rank of vice-admiral and flying his flag on the Orient.

As soon as the land troops were disembarked, he was reputedly ordered by Bonaparte either to anchor in the port of Alexandria or to return quickly to France, Malta or Corfu.

Citing concern that the Alexandria harbour was too shallow and difficult to enter for his large warships, and unwilling to leave Egypt until the situation of the French army was secured, he instead opted to anchor in Aboukir Bay to await the British.

[2] Knowing the poor quality of his ships and crews, he preferred to guard a defensive position than take the offensive and he refused to weigh anchor when Horatio Nelson attacked his fleet on the evening of 1 August 1798.

In the ensuing Battle of the Nile, the Orient fought HMS Bellerophon, causing her major damage but receiving little support, especially from the rearguard under Denis Decrès and Villeneuve.

[5] Brueys was criticised in France for remaining at anchor right up until the moment of the attack, but Bonaparte replied to such criticism by saying "If, in this disastrous event, he made mistakes, he expiated them by his glorious end".