The bulk of the Army of the Orient that returned to France returned on British ships. British and Ottoman expeditionary forces had landed in Egypt in March 1801. The French fought long, losing a series of battles through that spring and summer in the hopes that peace negotiations between Britain and France would salvage French of Egypt. Such hopes were in vain, but the continuing Anglo-French negotiations- which would culminate in the Amiens peace- did give the French favorable terms of surrender in Alexandria in August 1801 (although they could have gotten the same terms in June when Cairo fell). The French forces, which were larger than the British expected, were to be repatriated back to France via British ships. The French had to surrender all of the cultural treasures their expedition uncovered, which included the Rosetta Stone, but returned with their arms and ten artillery pieces.

The British rationale for shipping back the Army of the Orient was an expedient solution. There were hints of renewed fighting on the continent and little need to maintain a large expeditionary force in Egypt. Guarding the French troops in Egypt or sending them to Britain would have been labor and resource intensive, especially since it appeared that peace was around the corner.