Although powerfully fortified against attack by sea, Toulon's extensive defences on the landward side of the city had been designed to be held by substantial numbers of troops, something the allies conspicuously lacked.
Political disputes with the Italian allies prevented reinforcements reaching the defenders and the defeat of Royalist forces elsewhere in France gave strength to the besieging army.
Hood ordered an evacuation and as the Allied forces staged a fighting withdrawal British Captain Sir Sidney Smith and Spanish Don Pedro Cotiella volunteered to lead boat parties into the harbour to destroy the French fleet, which remained at anchor.
For reasons that remain unclear, but which British historians have sometimes attributed to treachery, the Spanish failed to destroy the ships they were tasked with, and as the force withdrew detonated two powder hulks they were instructed to sink dangerously close to Smith's men, killing several.
As Smith burnt the fleet, ships from the British squadron at Toulon successfully removed the Allied garrison as well as more than 14,000 Royalist refugees.
By the summer of 1793 the increasing radicalisation of the French Assembly had alienated much of Southern France, and a series of Royalist uprisings broke out in August.
Republican shore batteries exchanged fire with Royal Navy ships during which HMS Princess Royal suffered heavy casualties in an ammunition explosion, and on 30 September Republican troops under Captain Napoleon Bonaparte captured the hill of Pharon, only to be driven off the following day by a combined force of British, Spanish, Neapolitan and Sardinian soldiers under Lord Mulgrave.
[22] These ships contained the gunpowder stores for the entire fleet and due to the danger of explosion were anchored in the outer roads, some distance from the city.
Smith's boats approached the dock gates, which had been barred against attack and manned by 800 former galley slaves freed during the retreat whose sympathies were with the advancing Republicans.
[23] Dockyard workers, rapidly abandoning Royalist insignia, also attempted to block Smith's operation but were successfully locked out of the Arsenal.
As darkness fell Republican troops reached the shoreline and contributed musketry to the fusillade, Smith replying with grape shot from his boat's guns.
[27] With the fires spreading through the dockyards and New Arsenal Smith began to withdraw, his force illuminated by the flames as an inviting target for the Republican batteries.
[29] The gun batteries defending the Arsenal, reported sabotaged by French Royalist troops, had been taken intact and opened a heavy fire on the boat parties.
The French Republican prisoners on board had initially resisted British efforts to burn the ships, but with the evidence of the destruction in the arsenal before them they consented to be safely conveyed to shore as Smith's men set the empty hulls on fire.
[30] Once the British and Spanish boat parties had departed, the galley slaves opened the dockyard gates, allowing dock workers and Republican troops to enter the Arsenal.
[31] With all available targets now on fire or in French hands, Smith withdrew once more, accompanied by dozens of small watercraft packed with Toulonnais refugees and Neapolitan soldiers separated during the retreat.
Although his force was well within the blast radius, on this occasion none of Smith's men were struck by falling debris and his boats were able to retire to the waiting British fleet without further incident.
[23] The allied troops embarked in good order, protected by the rearguard of Sardinian soldiers under Major George Koehler and fire from the frigate HMS Romulus.
[36] In the aftermath of the fall of Toulon, Deputies Moyse Bayle and Louis-Marie Stanislas Fréron conducted a campaign of ideological terror against the population, executing an estimated 6,000 civilians and recruiting an army of 12,000 masons from across Southern France to destroy much of the city as punishment for the rebellion.
British historian William Laird Clowes noted wryly that "the excitement and danger of the situation seem to have proved too much for the Spaniards", later accusing them directly of "jealousy and treachery".
[28] Smith's parties had been much more successful than their Spanish counterparts, the burning Vulcan contributing to the total destruction of six ships of the line in the New Arsenal and damaging five more.
His boarding parties also seized and destroyed the prison ships Héros and Thémistocle without unnecessary loss of life and caused considerable damage to shore installations.
[40] Smith's Oxford Dictionary of National Biography entry notes however that "The British had indeed missed an unprecedented opportunity to weaken French naval power.