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Neapolitan campaign

Nelson was dismayed by Lord Spencer 's decision, and declared that he would rather have received no title than that of a mere barony. He was, however, cheered by the attention showered on him by the citizens of Naples, the prestige accorded him by the kingdom's elite, and the comforts he received at the Hamiltons' residence. He made frequent visits to their residence to attend functions in his honour, or tour nearby attractions with Emma, who was almost constantly at his side and with whom, by now, he had fallen deeply in love.

Orders arrived from the Admiralty to blockade the French forces in Alexandria and Malta, a task Nelson delegated to his captains, Samuel Hood and Alexander Ball. Despite enjoying his lifestyle in Naples—even while judging it to be a "country of fiddlers and poets, whores and scoundrels", which he found less than desirable —Nelson began to think of returning to England. However, King Ferdinand IV, had just faced an extended period of pressure from his wife, Maria Carolina of Austria, who was advocating for an aggressive foreign policy towards France; a country which, five years earlier, had beheaded her sister, and its queen, Marie Antoinette. Sir William Hamilton was joined in agreement with Queen Maria Carolina, and the King finally agreed to declare war on France.

The Neapolitan Army, led by the Austrian General Mack, and supported by Nelson's fleet, retook Rome from the French in late November 1798. The French regrouped outside Rome and after being reinforced, routed the Neapolitans. In disarray, the Neapolitan army fled back to Naples, with the pursuing French close behind. Nelson hastily organised the evacuation of the Royal Family, several nobles, and British nationals—including the Hamiltons. The evacuation got underway on 23 December and sailed through heavy gales before reaching the safety of Palermo, on 26 December.

With the departure of the Royal Family, Naples descended into anarchy, and news reached Palermo, in January, that the French had entered the city under General Championnet and proclaimed the Parthenopaean Republic. Nelson was promoted to Rear-Admiral of the Red on 14 February 1799, and was occupied for several months in blockading Naples, while a popular counter-revolutionary force, under Cardinal Ruffo, known as the Sanfedisti, marched to retake the city. In late June, Ruffo's army entered Naples, forcing the French and their supporters to withdraw to the city's fortifications, as rioting and looting broke out amongst the ill-disciplined Neapolitan troops.

Dismayed by the bloodshed, Ruffo agreed to a capitulation with the Jacobin forces, which allowed them safe conduct to France. Nelson arrived off Naples on 24 June, to find the treaty put into effect. His subsequent role is still controversial. Nelson, aboard Foudroyant, was outraged, and backed by King Ferdinand IV, he insisted that the rebels must surrender unconditionally. They refused. Nelson appears to have relented and the Jacobin forces marched out to the awaiting transports. Nelson then had the transports seized.

He took those who had surrendered under the treaty under armed guard, as well as the former Admiral Francesco Caracciolo, who had commanded the Neapolitan navy, under King Ferdinand IV, but had changed sides during the brief Jacobin rule. Nelson ordered his trial by court-martial and refused Caracciolo's request that it be held by British officers. Caracciolo was also not allowed to summon witnesses in his defence and was tried by royalist Neapolitan officers. He was sentenced to death. Caracciolo requested to be shot rather than hanged, but Nelson, following the wishes of Queen Maria Carolina, a close friend of Lady Hamilton, also denied this request, and even ignored the court's request to allow 24 hours for Caracciolo to prepare himself. Caracciolo was hanged aboard the Neapolitan frigate Minerva at 5 o'clock the same afternoon.

Nelson kept the bulk of the Jacobins on the transports and began to hand hundreds over for trial and execution, refusing to intervene, despite pleas for clemency from both the Hamiltons and Queen Maria Carolina. When the transports were finally allowed to carry the Jacobins to France, less than one-third were still alive. On 13 August 1799, in reward for his support of the monarchy, King Ferdinand IV gave Nelson the newly created title Duke of Bronte, in the peerage of the Kingdom of Sicily, as his perpetual property, as well as the estate of the former Benedictine abbey of Santa Maria di Maniace—which he later transformed into the Castello di Nelson —situated between the comunes of Bronte and Maniace, later known as the Duchy of Nelson.

In 1799, Nelson opposed the mistreatment of slaves held in Portuguese galleys off Palermo and intervened to secure their release. Nelson petitioned the Portuguese commander Marquiz de Niza:

The marquis acquiesced to the unusual request, allowing twenty-four slaves to be transferred to HMS Bonne Citoyenne; their blessings to Nelson ringing out across the harbour, as their names were added to the sloop's already crowded muster book.