The Bellerophon had been fighting L'Orient single-handed for nearly an hour when, around 8 pm, her mizenmast was shot away and came crashing across the stern. Shortly afterwards her mainmast toppled and fell across the starboard side of the upper deck, most of it coming to rest on the booms and the forecastle. The mainmast brought down with it the topmast, the yards and heavy canvas sails, the tarred rigging of the shrouds, and a tangle of ropes and heavy wooden blocks. It killed Lieutenant Lander and several seamen and produced a scene of chaos on deck. Robert Cathcart, the third lieutenant, now left his post on the main deck and came up to the quarterdeck to take over command of the ship. There was no question of surrendering and the gun crews continued to load and fire, but the wreckage of the two fallen masts had to be cleared, and a new danger had arisen which was potentially even more hazardous than the bombardment of cannon and musket shot from L'Orient. This was a fire which had broken out in the stern part of the French flagship.
The Alexander and Swiftsure had been delayed by their reconnaissance of the port of Alexandria and came late on the scene. When they did so they headed for L'Orient. The Alexander was the first to arrive. She cut through the line of French ships astern of the flag-ship and anchored off her in a good position to do maximum damage. She was able to fire into the vulnerable stern of L'Orient, her shot smashing through the stern galleries and stern windows and causing carnage the length of the ship. This onslaught started a fire in the stern cabin which rapidly spread to the poop and the rest of the ship. A wooden warship of this period was a floating fire hazard. Almost everything was highly inflammable at the best of times but the Mediterranean sun had dried out sails and rigging, and softened the tar used to caulk the planking of decks. The liberal use of paint and tar as preservatives increased the fire risk and the barrels of gunpowder stored in the magazine had the potential to act as a bomb which could destroy the entire ship. As the fire on L'Orient spread out of control the disabled Bellerophon alongside her was in an exceedingly dangerous position. The ship's log provides a glimpse of what happened next: At 9, observing our antagonist on fire on the middle gun deck, cut the stern cable and wore clear of her by loosing the spritsail - shortly, the fore mast went over the larboard bow. Employed clearing the wreck and putting out the fire which had caught in several places of the ship.'
This is a typically terse and shorthand account of an exceedingly difficult operation. With two of her masts gone, her deck a shambles, and many of her crew dead or wounded, it was not easy for her one remaining officer to get the ship clear of the burning flagship. After the anchor cable had been hacked through with axes the ship was free to drift but until she got some sail up she could not be manoeuvred clear of L'Orient. Lieutenant Cathcart dared not risk setting any sail on the foremast because most of the supporting rigging had been shot through. He therefore ordered the men to set the spritsail, a relatively small sail which was set on a yard from the ship's bowsprit. Even this put too much strain on the foremast because, as the Bellerophon gathered way, the mast toppled forward and came crashing down. The ship was now totally dismasted but, to the relief of her shattered crew, she continued to move slowly clear of L'Orient and out of the line of battle. The map in Clarke and M'Arthur's biography of Nelson shows her track. What it does not show is how the Bellerophon nearly became the victim of friendly fire.
The Swiftsure was bearing down on the enemy under a press of sail when her commander, Captain Hallowell, saw a dismasted ship moving out of the line of battle. In the darkness it was difficult to identify her but he noted that she was not displaying the four lanterns at her mizen which were the distinguishing lights of a British ship. The Reverend Cooper Willyams, who was the chaplain on board the Swiftsure, later described how Captain Hallowell, presuming the ship to be the enemy, felt inclined to fire into her,
but as that would have broken the plan he had laid down for his conduct, he desisted: and happy it was that he did so; for we afterwards found the ship in question was the Bellerophon, which had sustained such serious damage from the overwhelming fire of the French Admiral's enormous ship L'Orient, that Captain Darby found it necessary for him to fall out of action, himself being wounded, two lieutenants killed and near two hundred men killed and wounded. His remaining mast falling soon after, and in its fall killing several officers and men (among the former was another of his lieutenants) he was never able to regain his station. At three minutes past eight o'clock the Swiftsure anchored, taking the place that had been occupied by the Bellerophon.
In fact the Swiftsure did not anchor in the Bellerophon's place but selected a spot somewhat ahead of L'Orient. From there she could direct her fire at the bows of the burning flagship and at the stern of Le Franklin. She was in no immediate danger from the flaming debris falling from L'Orient because she was upwind of her and Captain Hallowell reckoned that if and when the flagship did explode 'the greater part of the fragments would naturally be projected over and beyond her.' Meanwhile the Bellerophon was moving further and further away from the battle and into the darkness beyond, her progress impeded by the shattered masts, torn sails and rigging trailing next to her battered hull. The most urgent task of her crew was to extinguish the fires which had broken out and when this had been done they turned their attention to cutting away the wreckage of the three masts. It was while they were hacking at the chaotic jumble of ropes and sails that the French flagship exploded.
Admiral de Brueys was dead before his ship blew up. His heroism became a legend in the French Navy. He had been hit in the face and left hand by musket shot fired from the Bellerophon but he had the wounds bound up and continued to direct operations. Both his legs were then shot away but still he refused to leave the deck. According to some French accounts he had tourniquets tied around the stumps, got himself strapped in a chair and was heard to say that a French admiral ought to die on his own quarterdeck. His bravery proved fatal because he was in an exposed position. He was hit again, this time by a cannon ball which nearly cut him in two. His flag captain, Commodore Casabianca, was also mortally wounded. His young son refused to leave his side, and this later inspired the poem by Felicia Hemans with the familiar opening lines, 'The boy stood on the burning deck whence all but he had fled.' Father and son took to the water and were last seen clinging to a floating mast. Admiral Ganteaume, several other officers, and many of the crew also abandoned ship, realising that it was only a matter of time before the fire reached the gunpowder in the magazine.
Many accounts have survived of the devastating noise of the explosion, and numerous pictures were later painted showing the night sky illuminated by the blinding light at the centre of the blast as the great ship disintegrated. One of the most graphic descriptions of the scene was provided by a French onlooker who was several miles away in the town of Rosetta at the mouth of the Nile. Monsieur Poussieulque was Comptroller-General of the Eastern Army in Egypt and two days after the battle he wrote to a friend in Paris about the battle which he had witnessed. The ship carrying his letter, together with the latest despatches from Napoleon, was intercepted in the Mediterranean and nine weeks later the letter was published by The Times in London. Poussieulque described how he and his companions heard the firing of cannon at 5.30 in the evening: