Captain Horatio Nelson was at this time by no means favourably impressed by his future friend and comrade, and described Ball as a "great coxcomb".

Whenever Ball appeared in public, the passers-by in the streets stood uncovered until he had passed; the clamours of the market-place were hushed at his entrance and then exchanged for shouts of joy and welcome.

Napoleon's troops succeeded in entering Naples itself, forcing King Ferdinand IV to flee the city with his family.

Captain Alexander Ball succeeded in calming the situation, and this led to his eventual election as the President of the National Assembly that took place on 9 February 1799.

However, the increasingly precarious situation faced by King Ferdinand IV made Ball pass more powers to the British forces stationed in and around Malta.

Nelson wrote to Ball in January 1799: "...Respecting the situation of Malta with the King of Naples, it is this – he is the legitimate Sovereign of the Island: therefore, I am of opinion his Flag should fly.

The French were allowed to leave with full military honours, and after a few days Ball and the Maltese could enter the liberated capital.

Control passed to Major General Henry Pigot, whose tyrannical administration angered the Maltese, a fact noted in a letter Ball wrote to Nelson in June of the same year.

Nelson himself wrote back to Ball from the Baltic on 4 June 1801: "My dear, invaluable friend,... believe me, my heart entertains the very warmest affection for you, and it has been no fault of mine, and not a little mortification, that you have not the red ribbon and other rewards that would have kept you afloat; but as I trust the war is at an end, you must take your flag when it comes to you, for who is to command our fleets in a future war?...

I pity the poor Maltese; they have sustained an irreparable loss in your friendly counsel and an able director in their public concerns; you were truly their father, and, I agree with you, they may not like stepfathers....

The choice of Charles Cameron as Civil Commissioner in May 1801 did not remove these uncertainties, even though his presence assured the Maltese of the protection of the Empire.

After the Napoleonic Wars, through the Treaty of Paris of 1814, as ratified by the Congress of Vienna, Malta and all its dependencies passed under the jurisdiction of the British.