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When Alexandria harbour proved inadequate for his fleet, Brueys had gathered his captains and discussed their options.
Bonaparte had ordered the fleet to anchor in Aboukir Bay, a shallow and exposed anchorage, but had supplemented the orders with the suggestion that if Aboukir Bay was too dangerous Brueys could sail north to Corfu, leaving only the transports and a handful of lighter warships at Alexandria.
Brueys refused, in the belief that his squadron could provide essential support to the French army on shore, and called his captains aboard his 120-gun flagship Orient to discuss their response should Nelson discover the fleet in its anchorage.
Despite vocal opposition from Contre-Admiral Armand Blanquet, who insisted that the fleet would be best able to respond in open water, the rest of the captains agreed that anchoring in a line of battle inside the bay presented the strongest tactic for confronting Nelson.
It is possible that Bonaparte envisaged Aboukir Bay as a temporary anchorage: on 27 July he expressed the expectation that Brueys had already transferred his ships to Alexandria and three days later issued orders for the fleet to make for Corfu in preparation for naval operations against the Ottoman territories in the Balkans, although the courier carrying the instructions was intercepted and killed by Bedouin partisans.

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