When the Ottomans in Constantinople received news of the French fleet's destruction at Aboukir, they believed this spelled the end for Bonaparte and his expedition. Sultan Selim III decided to wage war against France, and sent two armies to Egypt. The Ottomans planned two offensives against Cairo: from Syria, across the desert of Salhayeh-Belbays-El Kankah, and from Rhodes by sea landing in the Aboukir area or the port city of Damietta.
In January 1799, during the canal expedition, the French learned of the hostile Ottoman movements and that they had seized the desert fort of El-Arich ten miles (16 km) from Syria's frontier with Egypt. Certain that war with the Ottoman sultan was imminent and that he would be unable to defend against the Ottoman army, Bonaparte decided that his best defence would be to attack them first in Syria, where a victory would give him more time to prepare against the Ottoman forces on Rhodes.
Before leaving Jaffa, Bonaparte set up a divan for the city along with a large hospital on the site of the Carmelite monastery at Mount Carmel to treat those of his soldiers who had caught the plague, whose symptoms had been seen among them since the start of the siege. A report from generals Bon and Rampon on the plague's spread worried Bonaparte. To calm his army, it is said he went into the sufferers' rooms, spoke with and consoled the sick and touched them, saying "See, it's nothing", then left the hospital and told those who thought his actions unwise "It was my duty, I'm commander-in-chief".
Antoine-Jean Gros (16 March 1771 – 25 June 1835), Baron Gros, also known as Jean-Antoine Gros, was both a French history and neoclassical painter.
However, some later historians state that Napoleon avoided touching or even meeting plague-sufferers to avoid catching it and that his visits to the sick were invented by later Napoleonic propaganda. For example, long after the campaign, Antoine-Jean Gros produced the propaganda painting Bonaparte visiting the plague-victims of Jaffa in 1804. This showed Napoleon touching a sick man's body, modelling him on an Ancien Régime king-healer touching sufferers from the "King's Evil" during his coronation rites – this was no coincidence, since 1804 was the year Napoleon Bonaparte crowned himself emperor.
From Jaffa the army set off for the coastal town of Acre. En route it captured Haifa and the munitions and provisions stored there, along with the castle at Jaffe, the castle at Nazareth and the town of Tyre. The siege of Acre began on 18 March but the French were unable to take it and it was here that the Syrian campaign came to an abrupt halt. The city was defended by newly created Ottoman infantry elites (Nizam-ı Cedid) under the command of Jezzar Pasha and was right on the coast, enabling it to be reinforced and resupplied by the British and Ottoman fleets
After sixty days' repeated attacks and two murderous and inconclusive assaults, the city remained uncaptured. Even so, it was still awaiting reinforcements by sea as well as a large army forming up in Asia on the sultan's orders to march against the French. To find out the latter's movements, Jezzar ordered a general sortie against Bonaparte's camp. This sortie was supported by its own artillery and a naval bombardment from the British.
With his usual impetuosity, Bonaparte pushed Jezzar's columns back against their own walls and then went to help Kléber, who was retrenched in the ruins with 4,000 Frenchmen and 20,000 Ottomans under his command. Bonaparte conceived a trick which used all the advantages offered him by the enemy position, sending Murat and his cavalry across the River Jordan to defend the river crossing and Vial and Rampon to march on Nablus, while Bonaparte himself put his troops between the Ottomans and the magazines.
These manoeuvres were successful, in what was known as the battle of Mount Tabor. The enemy army, taken by surprise at many points at once, was routed and forced to retreat, leaving their camels, tents, provisions and 5,000 dead on the battlefield.
These factors renewed the courage of the besieged and they pushed Bonaparte's force back, with stubborn fury on both sides. Three final consecutive assaults were all repulsed, convincing Bonaparte that it would be unwise to continue trying to capture Acre. He raised the siege in May and consoled his soldiers with the proclamation:
“ After feeding the war for three months in the heart of Syria with a handful of men, taking forty guns, fifty flags, 10,000 prisoners, razing the fortifications of Gaza, Kaïffa, Jaffa, Acre, we shall return to Egypt. ”
The French force's situation was now critical – the enemy could harass its rear as it retreated, it was tired and hungry in the desert, it was carrying a large number of plague-sufferers. To carry these sufferers in the middle of the army would spread the disease, so they had to be carried in the rear, where they were most at risk from the fury of the Ottomans, keen to avenge the massacres at Jaffa. There were two hospital depots, one in the large hospital on Mount Carmel and the other at Jaffa. On Bonaparte's orders, all those at Mount Carmel were evacuated to Jaffa and Tentura. The gun horses were abandoned before Acre and Bonaparte and all his officers handed their horses over to the transport officer Daure, with Bonaparte walking to set an example.
To conceal its withdrawal from the siege, the army set off at night. Arriving at Jaffa, Bonaparte ordered three evacuations of the plague sufferers to three different points – one by sea to Damietta, one by land to Gaza and one by land to Arish. During the retreat the army picked clean all the lands through which they passed, with livestock, crops and houses all destroyed by sword and fire and Gaza the only place to be spared, in return for remaining loyal to Bonaparte. To speed the retreat, Bonaparte also took the controversial step of killing prisoners and plague-stricken men along the way. His supporters argued that this was necessary given continuing harassment of stragglers by Ottoman forces.
Finally, after four months away from Egypt, the expedition arrived back at Cairo with 1800 wounded, after losing 600 men to the plague and 1200 to enemy action. In the meantime Ottoman and British emissaries had brought news of Bonaparte's setback at Acre to Egypt, stating that his expeditionary force was largely destroyed and Bonaparte himself was dead. On his return Bonaparte scotched these rumours by re-entering Egypt as if he was at the head of a triumphal army, with his soldiers carrying palm branches, emblems of victory. In his proclamation to the inhabitants of Cairo, Bonaparte told them:
“ He is back in Cairo, the Bien-Gardé, the head of the French army, general Bonaparte, who loves Mahomet's religion ; he is back sound and well, thanking God for the favours he has given him. He has entered Cairo by the gate of Victory. This day is a great day; no one has ever seen its like; all the inhabitants of Cairo have come out to meet him. They have seen and recognised that it is the same commander in chief, Bonaparte, in his own person; but those of Jaffa, having refused to surrender, he handed them all over to pillage and death in his anger. He has destroyed all its ramparts and killed all those found there. There were around 5,000 of Jezzar's troops in Jaffa – he destroyed them all. ”
At Cairo the army found the rest and supplies it needed to recover, but its stay there could not be a long one. Bonaparte had been informed that Murad Bay had evaded the pursuit by generals Desaix, Belliard, Donzelot and Davoust and was descending on Upper Egypt. Bonaparte thus marched to attack him at Giza, also learning that 100 Ottoman ships were off Aboukir, threatening Alexandria.
Without losing time or returning to Cairo, Bonaparte ordered his generals to make all speed to meet the army commanded by the pasha of Rumelia, Saïd-Mustapha, which had joined up with the forces under Murad Bey and Ibrahim. Before leaving Giza, where he found them, Bonaparte wrote to Cairo's divan, stating:
“ 80 ships have dared to attack Alexandria but, beaten back by the artillery in that place, they have gone to anchor in Aboukir Bay, where they began disembarking [troops]. I leave them to do this, since my intention is to attack them, to kill all those who do not wish to surrender, and to leave others alive to led in triumph to Cairo. This will be a handsome spectacle for the city. ”
First Bonaparte advanced to Alexandria, from which he marched to Aboukir, whose fort was now strongly garrisoned by the Ottomans. Bonaparte deployed his army so that Mustapha would have to win or die with all his family. Mustapha's army was 18,000 strong and supported by several cannon, with trenches defending it on the landward side and free communication with the Ottoman fleet on the seaward side. Bonaparte ordered an attack on 25 July and the Battle of Abukir ensued.
n a few hours the trenches were taken, 10,000 Ottomans drowned in the ocean and the rest captured or killed. Most of the credit for the French victory that day goes to Murat, who captured Mustapha himself. Mustapha's son was in command of the fort and he and all his officers survived but were captured and sent back to Cairo as part of the French triumphal procession. Seeing Bonaparte return with these high-ranking prisoners, the population of Cairo superstitiously welcomed him as a prophet-warrior who had predicted his own triumph with such remarkable precision.
The land battle at Abukir was Bonaparte's last action in Egypt, partly restoring his reputation after the French naval defeat at the same place a year earlier. However, with the Egyptian campaign stagnating and political instability developing back home, a new phase in Bonaparte's career was beginning – he felt that he had nothing left to do in Egypt which was worthy of his ambition and that (as had been shown by the defeat at Acre) the forces he had left to him there were not sufficient for an expedition of any importance outside of Egypt. He also foresaw that the army was getting yet weaker from losses in battle and to disease and would soon have to surrender and be taken prisoner by its enemies, which would destroy all the prestige he had won by his many victories. Bonaparte thus spontaneously decided to return to France. During the prisoner exchange at Aboukir and notably via the Gazette de Francfort Sidney Smith had sent him, he was in communication with the British fleet, from which he had learned of events in France. As Bonaparte saw (and later mythologised) it France was thrown back into retreat, its enemies had recaptured France's conquests, France was unhappy at its dictatorial government and was nostalgic for the glorious peace it had signed in the Treaty of Campo Formio – as Bonaparte saw it, this meant France needed him and would welcome him back.
He only shared the secret of his return with a small number of friends whose discretion and loyalty were well-known. He left Cairo in August 1799 on the pretext of a voyage in the Nile Delta without arousing suspicion, accompanied by the scholars Monge and Berthollet, the painter Denon, and generals Berthier, Murat, Lannes and Marmont. On 23 August 1799 a proclamation informed the army that Bonaparte had transferred his powers as commander in chief to General Kléber. This news was taken badly, with the soldiers angry with Bonaparte and the French government for leaving them behind, but this indignation soon ended, since the troops were confident in Kléber, who convinced them that Bonaparte had not left permanently but would soon be back with reinforcements from France. As night fell, the frigate Muiron silently moored by the shore, with three other ships escorting her. Some became worried when a British corvette was sighted at the moment of departure, but Bonaparte cried "Bah! We'll get there, luck has never abandoned us, we shall get there, despite the English."
On their 41-day voyage back they did not meet a single enemy ship to stop them, with some sources suggesting that Bonaparte had purchased the British fleet's neutrality via a tacit agreement, though others hold this unlikely, since many would argue that he also had a pact with Nelson to leave him to board on the Egyptian coast unopposed with the fleet bearing his large army. It has been suggested that Sidney Smith and other British commanders in the Mediterranean helped Napoleon evade the British blockade, thinking that he might act as a Royalist element back in France, but there is no solid historical evidence in support of this conjecture.
On 1 October Napoleon's small flotilla entered port at Ajaccio, where contrary winds kept them until 8 October, when they set out for France. When the coast came in sight, ten British ships were sighted. Contre-amiral Ganteaume suggested changing course towards Corsica, but Bonaparte said "No, this manoeuvre would lead us to England, and I want to get to France.". This courageous act saved them and on 8 October 1799 (16 vendémiaire year VIII) the frigates anchored in the roads off Fréjus. As there were no sick men on board and the plague in Egypt had ended six months before their departure, Bonaparte and his entourage were allowed to land immediately without waiting in quarantine. At 6 pm he set off for Paris, accompanied by his chief of staff Berthier. He stopped off at Saint-Raphaël, where he built a pyramid commemorating the expedition.
The troops Bonaparte left behind were supposed to be honourably evacuated under the terms of a treaty Kléber had negotiated with Smith in early 1800, but British Admiral Keith reneged on this treaty, sending an amphibious assault force of 30,000 Mamlukes against Kléber.
Command of the French army passed to General Menou, who held command from 3 July 1800 until August 1801. Menou's letter was published in Le Moniteur on 6 September, with the conclusions of the committee charged with judging those responsible for the assassination:
Under continual harassment from the new Anglo-Ottoman land offensive, defeated by the British in the Battle of Alexandria on March 21, and at Fort Julien in April and then besieged in Alexandria from 17 August – 2 September 1801, Menou eventually capitulated to the British.
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