Hallowell was still in command of "Swiftsure" in 1798, when he was ordered to join Horatio Nelson's squadron, watching the French fleet at Toulon. After the French escaped and captured Malta in June, and invaded Egypt in July, Nelson and his fleet pursued them, eventually locating them anchored in Aboukir Bay on 1 August. "Swiftsure" was not initially with the fleet, having been ordered by Nelson to reconnoitre Alexandria, before the French had been discovered. He arrived on the scene after dark and moved into the bay to attack. The darkness and the smoke made it difficult to tell which ship was British and which was French, so Hallowell decided to hold fire until he had anchored and prepared his ship. As he moved closer, a darkened ship was spotted standing out of the action. Hallowell determined her to be French, but decided to hold to his original plan and passed her by. The ship was in fact , which had gone up against the much larger 110-gun French first rate "Orient" earlier in the battle, until being dismasted and forced to drift out of the action.