“The city, most of whose population was Christian, was an important stop-over on the road to Acre…the French had to take command of it if they wanted to maintain their line of communication with Egypt and receive reinforcements.”. Gueniffey, p. 481
“Jaffa was built on a hill … crowned with a small citadel surrounded by a crenelated wall without a moat, only four meters high and not more than a meter thick – hardly more than “garden wall” as Volney put it.”. Volney, Voyage en Égypte et en Syrie, I: pp. 116-117, Gueniffey, p. 481
The storm of Jaffa is well-known, in short, everyone the French divisions of Lannes and Bon came across inside the streets of Jaffa or the port, respectively, were massacred indiscriminately. The massacre, pillage and rapine continued for between one and four days depending upon the source. Gueniffey, p. 481-82 Bonaparte’s aides de camp, Eugène de Beauharnais and Crozier, accepted the surrender of the remnants of the garrison that had taken refuge in the citadel. Bonaparte flew into a rage (Guenniffey and Dwyer, both citing contemporary sources) and after much deliberation ordered them to be taken away and shot - or rather, once ammunition had run out, bayoneted.
“in war as in politics, every evil, even if it abides by the rules, is excusable only insofar as it is absolutely necessary; everything else in life is a crime.” . Regenbogen, Napoléon a dit, 18, Gueniffey, p. 484.
Gueniffey continues that Bonaparte had previously summoned the commander of El-Arish to surrender citing the laws of war and, more specifically, the law that stipulated “the garrison of a city must be killed” ironically some of the defenders of El-Arish were to be found in Jaffa and their betrayal of Bonaparte’s clemency became “his soundest argument” to support their execution … and punish them, not as guilty, but as potentially guilty”.
After some careful considerations of 'le droit des gens' set out by Vattel, Gueniffey concludes “[the prisoners of Jaffa] were not put to death solely because “it was more convenient” but also to “produce an effect”.” to deter further opposition to French occupation in general and most specifically as a warning to the garrison of St. John of Acre.
Bonaparte could rule at home with moderation as his rivals or detractors would be in full knowledge that he would not hesitate to order to death those who presented a challenge to the safety of the French army or – presumably by extension – the French nation and most particularly the state. Gueniffey, pp. 486-88
Vattel, Emer. de, Le droit des gens ou principes de la loi naturelle appliqués à la conduite et aux affaires des nations et des souverains, 1758 (my emphasis)