Following the Battle of the Nile, Nelson went in HMS Vanguard to Naples, then one of Britain's few allies in the Mediterranean basin. He arrived on 22 September 1798 to a rapturous welcome. His stunning victory appeared to have changed the course of the war. The invincible French had received their first major check and the Mediterranean had been transformed into an English lake by the elimination of the French fleet. Later in the year, urged on by Nelson, King Ferdinand of Naples marched his army north, captured Leghorn and entered Rome in triumph. Feeling that his task in the Mediterranean was complete, Nelson began to talk of returning home to England.

But his sense of completion was premature. The French quickly struck back. Within a week, Ferdinand had been forced to leave Rome, and by the middle of December, the French army was threatening Naples itself. Ferdinand fled, with all his court and treasure, in Nelson's flagship HMS Vanguard, to his second capital of Palermo in Sicily, leaving his Neapolitan subjects to their fate. On 27 January 1799 the French armies entered Naples and the Parthenopean Republic was proclaimed. Nelson felt obliged to help the King to recover his throne, so becoming directly involved in a very bloody and vicious civil war. He was personally implicated in some ugly incidents, such as the trial and summary execution of one of the republican leaders, Commodore Franceso Carraciolo, and the surrender for brutal execution of a number of other key Neapolitan revolutionaries.

Nelson's close involvement with Naples in 1798/9 was the most controversial period in his career, even during his lifetime, and it has remained controversial ever since. A more cautious man might have remained detached, offering help from a distance. But such was not Nelson's way: impulsive and eager as always, he threw himself into the thick of the fray, just as he had done at Cape St Vincent and again at Tenerife. This time, however, it was not his body that suffered but his reputation. Questions were asked in Parliament about his conduct in Naples, and the debate about his complicity in the atrocities, and whether or not he should be held responsible for them, has continued ever since.