Mordechai Gichon, Tel-Aviv University
When composing his memoirs in St. Helena, Napoleon wrote: "Jaffa is the only harbour on the road from Damiette to here (central Palestine). The possession of this harbour was vital for the upkeep of the naval communications with Egypt, so as to enable the unloading of provisions for the army and the siege guns that were transported by ship. It would have been contrary to all rules of prudence to move against Jerusalem prior to the conquest of Jaffa." (Napoleon I, Commentaires).
By recognizing the necessity of capturing Jaffa first, Napoleon was doubtlessly motivated also by the fear that the British, with their absolute mastery of the sea after their victory at Abukir, would seize the opportunity to land Turkish forces at this port and cut his communications with the Egyptian bases.
Moreover, Napoleon was loath to be entangled in fighting in the Judean mountains. Careful perusal of the Bible and Josephus had convinced him of the difficulties of achieving success in these parts, with limited forces against a determined enemy recruited largely from the autochtone mountaineers.  As far as we can reconstruct, his overall strategic planning - the penetration into the mountains - was conceived as a final step, after the plains and the key fortress of St. Jean d'Acre (Acco) were subdued. The outcome of his oral and written communications with the governor and the community leaders in Jerusalem indicate that he looked forward to a peaceful entry, once above goals had been achieved. 
The French army, that on February 1st 1799 had left for Palestine to forestall a Turco-British invasion through the Palestinian land-bridge, reached the outskirts of Jaffa on March 3rd. The French forces, 13,000 men strong, comprised 4 infantry divisions with a strength of about 1000 men and only 1 cavalry division of 800 horses. Aside from those supporting and technical units incorporated in the divisions, there were major contingents of artillery, engineers and medical personnel, that came directly under the command of the general-en-chef's headquarters. That headquarters also had direct command over the guides, an elite unit created in Egypt for special tasks and mainly for reconnaissance. 
The primary investment of Jaffa was made by the division of General Kleber, who, on the evening of that day, took over the task of shielding the besieging forces from hostile interference and deployed along the shores of the river Yarkon, 10 kms north of the town.
The eastern flank was guarded by Reynier's division. The latter had remained in the town of Ramla, occupied the day before, whence Reynier observed the Judean piedmont, to the east of the plains. Two divisions were charged with the actual siege operations, the one of Lannes, operating in the south and south-east, and the one of Bon, investing the north and the east - see map, [fig.1]
Several French officers have provided us in their diaries and memoirs with considerable details about the physical aspects of Jaffa and its immediate surroundings on the eve of the siege. Suffices to quote the journal of Detroye:
All writers of reminiscences stress the abundance of these plantations and their irrigation systems that provided ample water for the besiegers.
To complete the description, we need mention the citadel of 17th century date, built on the highest point and perching over the steep ascent from the harbour. The latter was no more than a narrow jetty, connecting with a line of reefs ("Andromeda's rocks"), which ran parallel to the then unwalled sea shore and afforded anchorage to crafts up to 100 tons only. The town itself was a maze of narrow lanes, lined by some houses, up to 4 stories high, the flat roofs of which proved excellent positions for the defenders' marksmen.
The garrison of Jaffa, 4,000-5,000 men strong, was commanded by Akhmad Agha. There is no saying whether some of the about 8,000 inhabitants took active part in the town's defense. Akhmad Agha's troops comprised Mughrabins (north-west Africans), Albanians and Sudanians, as well as Mameluks from the forces of Ibrahim Bey, that had withdrawn from Egypt, and, at least according to the French official sources, the Ottoman garrison of El Arish, which had surrendered to Napoleon under oath not to take up arms anymore against the French during the current conflict. 
Of importance also was the presence of a unit of Turkish field artillery that comprised 30 guns and which, before the deterioration of the Franco-Ottoman relations in 1797, had been specially trained by French advisers. This unit was part of the Turkish invasion force of Egypt, which had begun its piecemeal assembly in Palestine. It is possible that in addition there were 40-50 guns that belonged to the permanent armament of the town defenses. However, it seems that the maximum number of serviceable pieces of ordnance, made use of by the defenders, did not exceed 50 at most. 
Napoleon to be exact, at that time still addressed as Bonaparte arrived at 3 o'clock of the third day of March before the town walls, and immediately commenced an all-round reconnaissance to decide upon his plan of action. At the same time, reconnaissance parties of the corps of artillery and engineers, as well as of the divisions concerned, tried to gain the information necessary to them to implement the general plan decided upon. 
Napoleon correctly considered his main problem as that of the shortness of available time. The expedition had to be planned as what we, in modern parlance and with a view to the ways and means at disposal, would call a "Blitzkrieg" -like campaign. He had to break the Ottoman forces marching down Syria, so as to be back in Egypt in time to confront the expected debarkation of the Turkish invasion forces there. According to the conditions of the weather and the sea, this ship-borne arm of the huge pincers to envelop the French was due to disembark in the bay of Abukir in May-June of the selfsame year. Thus Napoleon had no more than 8 to 10 additional weeks to complete his conquest of Palestine and to arrange for its defense. Two precious weeks had unexpectedly been lost by the siege of El-Arish, and now he had to try and make up for the lost time. 
To get an as exact as possible view of the town defenses, Napoleon rode up close to the walls, and, by sheer luck, escaped being shot to death, when a sniper's bullet pierced his high hat.  These reconnaissances established the absence of a moat and other fortifications, and the trace of the walls was of the -in Europe- medieval, pre-gun pattern. On the other hand, the dense fruit-tree groves afforded good cover from view.
Accordingly, Napoleon decided to take the risk of dispensing with regular siege works, calculating, that even without interference, the construction of a single parallel with proper approaches and securely defended battery positions would demand a week's labor. Instead, he resolved to make maximum use of the tree cover and the undulating ground, to push his artillery up to 150 meters from the walls and to assemble his assault forces not much farther away, while the rest of the forces were deployed out of immediate harm's way. 
Lannes in the southern sector was assigned the task of the main attack, and Bon the task of the secondary effort only, in spite of the apparent greater weakness of the walls there. The reason for this was not only to have Bon act as a mere diversion, in spite of the little artillery support planned for the northern sector (see below), but to give his troops a real chance to penetrate into the town, while the defenders' attention was drawn to the opposite direction. It stands to reason that Napoleon wisely contemplated the alternative to switch efforts if need arose. 
The general headquarters was placed on the border of the divisional sectors in a large rainwater pond (site of to-day's Bloomfield stadium), shielded by citrus groves.
Under cover of night, between the 3rd and the 4th of March, work commenced- the erecting of five batteries, four against the southern wall and one in support of the northern sector.13 The artillery park at Napoleon's command consisted only of field pieces, mostly of 12, 8, 6 and 3 "pouces" (=inches of 2.7 cm), of howitzers of 6 pouces and of 6-pouce mortars,14 since the heavy artillery had all been loaded for transfer to Acre bay onto the ships of the flotilla commanded by captain Standelet, and onto the freighters that had been collected for that purpose in the Egyptian harbors. Those ships were only just then commencing their journey north, without the means of contact with the land forces, and Napoleon was compelled to make do with the lighter ordnance at his command. However, he did not seem to have been unduly worried.  Most probably, the outward appearance of these antiquated walls revived his confidence in the description of M. de Volney, who, in 1784, had called the ramparts of Jaffa "mere garden walls."
The reliance on Volney may sound strange, since it had been the cause for the severe reverse at El-Arish and had been among the reasons why Napoleon had thought he could do without the heavy artillery all along the Palestinian coast up to St. Jean d'Acre. It is however a human fallacy, even of the most outstanding persons and certainly in their formative years, to surrender under stress to a modicum of wishful thinking when forming plans and to rely on that information which suits best their ideas. Whatever his actual reasoning, Napoleon had convinced himself of the practicality of his planning.
The breach battery, consisting of four guns of 12 inches each and of two mortars, was placed among the trees, at a distance of about 200 meters from the walls. It had the aim of effecting two breaches, one in the center of the southern wall face and one in the south-east corner tower. The exact spot of the former was chosen so as to attain the strong, high buildings just behind the wall and to turn them into an immediate strongpoint to secure the hold of the breach and as a base for further penetration. Three further batteries, all that could be spared other than regimental pieces of the screening divisions, were erected somewhat to the rear and to the sides of the breach battery. This provided counter-battery and harassing fire in support of the former and covered the ramparts to the side of the breaches during the assault.
The northern battery had, in addition to its task of supporting the efforts of Bon, the special mission of covering the entrance to the harbour and preventing the escape of any vessels so as to make them French prizes. The compelling need for naval craft and freighters even of small size had been painfully taught to Napoleon and his basically "land-lubber" staff, after having been confronted with the necessity to maintain their levant base without all the ships lost at Abukir. Anticipating the chronological order of things, we note that the battery succeeded indeed to prevent the escape of a convoy of Turkish supply craft, that had entered the harbour on the 9th of March, unsuspecting the French presence.
The task of erecting the batteries and the infantry positions for their close protection and support, of constructing approaches and communication tracks and trenches to- and between them, their fortification with gabions and fascines, all this was not finished until the dawn of the 7th of March. 
The Turks did not sit idle all this time. While Mameluk and other forces harassed the build-up of the siege forces along the road and tracks from Ramla to Jaffa, troops from its garrison tried to impede the progress of the siege works. 
A typical example of the activities of the former is the ambush of a French reinforced platoon on forage north-west of Ramla. In spite of their protection by a screen of camel corps troopers, the foragers were completely surprised, 12 men were killed and most of the others were injured. More serious for the progress of the preparations of the siege were the sallies of the defenders. Making use of their better knowledge of the terrain, they surprised the French working parties that erected the gun positions, and succeeded in demolishing part of the work already done. Their task was eased by the fact that many of the tracks between the plantations were shielded on both sides by thick hedges, often mimosas, which permitted excellent cover from view. In his quest for saving time, Napoleon had underestimated the advantage of the poor all-around visibility to a resolute foe while attacking the unconnected French positions. The concerted series of major sallies, that took from noon to sunset of the 6th of March to be repulsed definitely, succeeded to damage most of the battery positions, to capture a substantial quantity of siege tools and small arms and to inflict a certain number of fatal casualties.  Even threats to the French western flank, from the direction of the sea, were not overlooked. Raiding parties landed once or twice on the dunes, but did not resolutely press their advantage. Later, after Lannes had moved one of his half-brigades more to the west so as to react to these landings more quickly, Akhmad Agha contented himself with using his boats for observation only. The French however wisely manned the Sheikh's tomb (santon) on the edge of the dunes with a permanent guard.
Yet, in spite of all interference, Napoleon did not lose his grip.  His sense of urgency was communicated to all his forces. They succeeded during the night of the 6th not only to repair the damages and to complete the positions, but to strengthen and extend them, to mount the guns and to open fire on zero-hour: 0800 on the next morning, the 7th of March [fig. 2]. 
According to the general orders,  Napoleon envisaged three major phases: shooting the two breaches, mounting and securing the breaches, penetrating and stamping out opposition there. The fire plan for the artillery was drawn up by Napoleon as follows, commencing from the south-west (see: [fig. 2]):
The task of the break-in detail was to make the breach practicable for forces B and C, while the close-support detachment had to give it close protection and secure the foothold in the breach and its immediate surroundings.
The break-through force was to fan out from the breaches and establish two secure 'bridge-heads' in front of the breaching force as base and support for force C, which had to undertake the actual capture of the interior of the town. 
Division Bon received the order to stage diversionary assaults from the south, parallel to the general attack, and was issued with assault ladders to mount the wall in that sector.
The allocation of relatively strong forces for the mounting and penetration of the breaches resulted from Napoleon's feeling of the need to sustain the pressure of the assailants and even to increase it in face of what he estimated to be determined resistance. The experience gained during the uprising in Cairo and the siege of El-Arish had taught the French commander not to underestimate the oriental prowess in defense of fortified places.
Fire commenced at 0700 hours as planned, after the proposal to render the town had been rejected. The circumstances of this incident were a major cause for turning the sack following the conquest of Jaffa into an orgy of atrocities. In the early morning, Napoleon had dispatched an officer with a flag of truce, to offer honorable surrender and immunity from sack. To their horror, the consternated French witnessed, soon after the officer and the accompanying trumpeter had entered the city, the severed heads of both rise on lances over the gate, and their bodies cast over the walls. Cries for revenge spread throughout the army and the subsequent heavy fighting did nothing to dampen the enraged spirits. 
According to plan, the breach battery fired 20 shots per gun per hour, a good performance for well aimed fire in those days. However, until 1400 hours, the walls were not breached. The reason was not only the relatively light caliber of the guns and Volney's erroneous estimate of the town wall being unable to resist concentrated fire. The French plan had not taken into consideration the fact that in Jaffa, as in many other eastern places, the ground niveau was much higher inside than outside the walls. Ruins of the former epochs were not cleared away and cast out but leveled, so as to serve as ground floor and foundations for subsequent building. This caused the constant rising of the niveau inside the town as against extra muros.  It therefore seems that the French gunners had not aimed high enough and that the strong and resilient fill-in absorbed and neutralized much of the shock of the cannon balls.
Only at about 1400 hours the effect of the cannonade began to show, and two small breaches appeared, most probably in the uppermost part of the target area above the ground-level line. However, time was getting short, since Napoleon did not want to postpone the assault until sunset (1730 hours), and therefore he ordered to concentrate all the breaching fire on the western breach only, so as to widen it sufficiently as quickly as possible.
Between 1500 and 1600 hours, the breach was judged to have become practicable. The breaching force jumped forward and, having succeeded in lodging a precarious foothold in the lower parts of the breach, began a slow fight upwards from the talus of fallen rubble into the breach proper. The troop was exposed to constant galling fire from the adjacent towers and from the high houses that towered over the breach. The support batteries, which tried to silence these Turkish positions, were incapable to achieve any effect. In consequence, the engineers who cleared the breach with tools and explosives, as well as the 22nd light half-brigade that made up the break-through force, suffered heavy losses. Colonel Lejeune, commander of the 22nd, was killed in the breach, and general Lannes personally took over command in the breach and gave brigadier-general Rambeau command over force A.
Rambeau, ably assisted by the engineers who excelled throughout all this action, broke into the house to the right of the breach [fig. 3], and after a fierce struggle, attained the roof. The Turkish opposition remained however so strong, that the grenadiers of Force B, that tried to exploit Rambeau's success, were twice thrown back. Even the mounting of a 3-pound cannon into the breach, with Rambeau joining into its manhandling under constant fire, did not bring the wished-for relief. The high house to the left enabled its defenders to cover the breach with a curtain of fire that the grenadiers were unable to penetrate. 
To annihilate this obstacle for further advance, Lannes hastily assembled a small force of pioneers and infantrymen under the command of engineer-captain Ayme. His first attempt to attain the house failed. On the second one he succeeded with only two pioneers. The general turmoil was at that moment so intense as to divert attention from this little group, and the fusillade from the upper stories of the house alone was sufficient to drown the noise created by their blowing an opening into one of the walls at street level. On entering, they found themselves in an underground cellar that was part of a much (?) earlier building, the lowest parts of which were incorporated in the foundations of the present structure, without any communication between the two. If the permanent occupants knew about the existence of these vaults, the soldiers covering the breach with a hail of well aimed shooting had no notion about them or they did not give them any second thought. This feeling of complete isolation from the outside happenings gave Ayme the idea that he had found a way to infiltrate into the town, unobserved by the defenders. All others having disappeared (hit or fled back), Ayme and his two intrepid comrades (?) crept back into the breach. Their luck held. Having arrived there, unhurt, they met the general-en-chef, who had taken up position at the foot of the breach, and he himself instantly directed a force of grenadiers to follow Ayme once more to the cellar. 
Although their general assault was broken, part of these reached the opening and entered. Exploitation of the vaults and passages revealed a small door, which, when forced, gave out to a deserted back lane. Thence, they commenced assaulting the defenders of the breach from the rear and enabled their gradual dislodgment.
As a matter of fact, the garrison of the house observed the breaking up of the back. They then took flight apparently without reporting this occurrence to any higher command echelons. In that way, direct and effective interference with mounting and penetrating, ceased! Napoleon, who had joined Lannes at the breach, succeeded in rushing all of force B into the town, followed by troops of force C. Darkness found the French clearing the ramparts, fighting from house to house and from story to story, with pioneers breaking walls and ceilings. 
The collapse of the defense was hastened by Bon's successful penetration into the town from the north. He had detected the weakest spot in the wall, which was where it ended at the sea shore. While some of his troops scaled the wall in the east, his main assault was along the shore.The men of the 1st battalion of the 22nd light infantry brigade were able to outflank and skirt the wall by wading through the water, while others scaled the walls. Once inside, the walls were cleared from within and the gross of the division assaulted the harbour. Since darkness had come, they were harassed only ineffectively by fire from the upper town and made themselves master of the whole harbour area.  Organized resistance ceased at about 2000 hours, after the citadel was taken (?)  and clearing-up operations began. However, some nuclei of defenders held out at least until noon on the following day, March 8th, even while the sack was raging all around. The Turkish standard was still flying near the harbour. This fact made some unsuspecting Turkish supply vessels enter the harbour, though the latter had already been captured and its approaches were commanded by Bon's artillery. They were swiftly taken and added to the meager fleet at Napoleon's command. Their cargo was a much applauded addition to the shrinking supplies of the French commissary. 
The mopping-up of the pockets of continuing resistance, together with the sack of the luckless city, turned soon into a nightmare of unbridled theft, rape, arson and murder, regardless of age, sex or nationality. Greek, Armenian and other local Christians, including French citizens, perished among the up to a thousand-five-hundred murdered. French officers, who tried to intervene, were themselves threatened, assaulted and wounded by the murderous frenzy of the troops, who seemed literally to have run amuck.  Suffices to cite Colonel Chalbrand: "Now commenced a scene of carnage, on which it is impossible to form an idea. My pen refuses to trace that horrible picture." 
In his letter to the Directoire, Napoleon expressed himself as follows: "...never has war appeared to me more terrible."  His sentiments are echoed by those of Wellington, following the capture of Budajoz and San Sebastian by his troops in 1812 and 1823 respectively.  Both declared their impotence to stem the fury of their soldiers until the following morning. 
The basic answer to the question as to what prompted these and similar excesses must be given by students of human nature and psyche. The then accepted rule that a city that had refused to an honorable surrender was liable to sack by the captors, was, of course, conductive to sundry excesses by the troops, the more so since their first reaction after the shock of battle was the quest for drink and drunkenness.
While the troops of Wellington were often pressed into service and included many criminal elements, most of them lacking any incentives other than esprit de corps, national pride and boundless loyalty to their commander,  the French prided themselves in the consciousness of the social and cultural mission that guided their arms. If we do not deny the de facto existence of these sentiments, the extremely brutal behavior of the troops at Jaffa is raising additional questions.
The answer may be in the general frustration of the troops that felt themselves intentionally misled before embarking on this expedition, as to the supposed idyllic situation to be encountered in Egypt of Pharaonic fame. Nor were they prepared mentally and psychologically to be shunned and hated by the locals as unbelievers that had come to conquer Islamic lands.  Moreover, in disputes between the French military and the Egyptian population, Napoleon took severe measures for punishment wherever he judged the French culpable, even if no solid proof for their accusations had been brought. The depart for the expedition to Palestine had been overshadowed by the summary execution of 10 grenadiers of the 32nd half-brigade, wrongly accused of the murder of 3 Egyptian women. The true culprits were discovered immediately after, and resentment was still running high, only partly overshadowed by the happenings of the campaign. 
The pent-up sentiments fanned by these and further factors reached their boiling point when the heads of the officer, bringing the French offer for surrender, and of his "trompette" were hoisted on the town walls. The Jaffa carnage seems thus to have been fanned by an accumulation of disappointments, frustration and rage. 
It seems that Napoleon, much like Wellington, judged himself incapable of stemming the tide at its height. He camped himself outside the town and order was restored only the next morning. 
Another, much deplorable episode was the shooting of the Turkish prisoners by explicit orders of the "general-en-chef." During the sack, a large number of defenders had retreated into a centrally sited building. It may have been the citadel, but this is not mentioned with certainty in any of the accounts.  Possibly recognizing Eugene de Beauharnais and Croisier (the former being Napoleon's step-son) as two of the general-en-chef's adjutants, they tended their surrender to those two officers. These, who had been sent to restore order, accepted it eagerly, so as to stop further bloodshed.46 The number of those who surrendered, quoted by our sources, fluctuates between 800-900 in Napoleon's commentaries, p.46, and 4000 in Bourienne's memoirs.  The true complement seems to have been around 2000, as the French commander admitted in his contemporary reports and letters.  Upon receiving the report of his adjutants, Napoleon immediately denied their authority to accept surrender on their personal judgment, and after some thought, he concluded that the alternatives of feeding and guarding this quantity of prisoners in Jaffa or escorting them to the rear in Egypt, were beyond the means of his invasion force. Nor did he trust their release upon oath of non- participation in future fighting, since part of the surrendered defenders had been among the garrison of El-Arish, which had capitulated on these terms before. 
Accordingly, he countermanded his adjutants' commitments and had all, or most of them, shot on the harbour beach, in spite of the protest of at least some of his staff and the general aversion of the troops to this order.  At the same time, even his greatest critics from among those present, such as Miot, proclaimed with hindsight their incapability of offering another way out of this dilemma, accepting in their memoirs the validity of Napoleon's reasoning.  Yet, in spite of this, any admirer of the "Great Corse," the greater his esteem, the more he must feel that a Napoleon should have been able to find a solution other than cold-blooded butchery. Bourienne and Krettly state that there had been a council of war, attended by the highest-ranking officers, that decided on the execution and that it was not Napoleon's unsolicited decision. There are no official documents to sustain the veracity of this event. De La Jonquiere has summed up the weighty arguments against its having been convened. 
It is in happier vein that we record the following episode of the aftermath of the capture of Jaffa, in spite of its most sinister background. One outcome of the sack was the large-scale infection of the troops by the plague, which in those days was endemic in these parts, owing to the climate and the poor standards of hygiene.  Soon, the Armenian convent, which served as base hospital, was filled with the sick, and when the malady was diagnosed, French medical staff and monks fled the place and abandoned the sick and afflicted. On receiving these news, Napoleon, with a couple of adjutants and the chief medical officers, Drs. Larrey and Desgenettes, hastened to the scene, and Napoleon made the round of the sick, touched them and told them not to believe having contacted the plague - how otherwise would he dare visit them and shake their hands!
It is said that this psychological therapy helped some of the victims to overcome the plague. Anyway, draconian measures were enacted to ensure a minimum of care for the inmates. 
This action connects with Napoleon's apparent personal attention to soldiers that collapsed during the traverse of the desert of Sinai. It is for each scholar to decide how much true compassion and how much pragmatic calculation were the motives that compelled Napoleon to these manifestations.
To complete Napoleon's activities in Jaffa, we shall mention here only very shortly, his diplomatic efforts. True to his future behavior, the general-en-chef immediately set out to try and gain political advantages from his military achievements. Letters and proclamations were directed at the Sultan, the various communities of Palestine and Syria and their leaders, Akhmad Jasar, the pasha of Acre and commander-in-chief (seraskir) of the Ottoman forces at that time.  All these aimed at paving the way for the complete occupation of the Holy Land by negotiation or by making alliances and contacts to ease further military conquest.
Among these was the contact with the Jewish communities in Palestine and Syria, the first de facto attention to the Jews as a potential factor in international policy in modern times. 
Finally, Napoleon issued directives for the administrative organization of the province of Jaffa to be similar to the one of Gaza. They were not implemented because of the shortness of his stay in the country and the local, mainly Muslim antagonism to the French republican ideas he tried to impose on the people, who were totally alien to these ideals and unprepared for their implementation. 
On the 14th of March, the French army continued its march northwards towards its goal, Acre.
The following lessons may be learned from our narrative, enumerated according to the chronological order of the occurrences they are relating to: