On 1 Nov 1803, the Malta garrison consisted of a total of 4,116 officers and men. There were: 137 Commissioned and Warrant Officers, 336 Non Commissioned Officers, 3,161 Rank and File fit for duty. 84 Commissioned and Warrant Officers were absent and 397 Rank and File were sick.
On 27 March 1803, the garrison at Alexandria was completely withdrawn in compliance with the terms of the Treaty of Amiens. Major General John Stuart, who had commanded the troops in Egypt, arrived in Malta on 27 March and left for Sicily on 14 May 1803.
On 26 March 1803, the 88th Foot and the Chasseurs Britanniques arrived from Egypt. The rest of the army reached Malta on 8 April. Many soldiers arrived from Alexandria in a desperate state. They lacked blankets, canteens, camp kettles and haversacks. All the Auberges, formerly the residences of the Langues of the Order of St John, were converted into barracks, but these held insufficient boards and trestles for the men to sleep on. The General Hospital, and the regimental hospitals in Valletta received 1,826 sick soldiers, 518 of which were suffering from Ophthalmia.
On 4 May 1803, General W. A. Villettes reported that he intended to send the troops to England on 12 May, despite a case of plague having erupted on the transports. Those destined to form part of the garrison, and who had completed quarantine at the lazaretto received pratique. The 48th Foot sailed immediately for England and the 63rd Foot left for Ireland. The troops from Egypt left Malta on 14 July with clean Bills of Health.
Plague had also broken out on board the transports of 10th Foot and amongst the French prisoners; fortunately the contagion did not spread to the civilian population. The French physicians in Egypt attributed the outbreak of plague to three principal causes: exposure to the weather, placing the soldiers in damp huts and barracks of any kind and over fatigue.
In 1803, General Villettes raised a Maltese levy. By July, only 900 men had been recruited, but by 14 Sept 1803, two Maltese Provincial Battalions were embodied, providing an extra 1,038 men to the garrison. These were in addition to the 170 men of the Companies of Coast Artillery stationed at Marsaxlokk and St Paul's Bay, and the 300 men of the Corps of Invalids and Police Guard.
The First Provincial Battalion, commanded by Marquis Paolo Parisi, occupied Fort Manoel; the Second Provincial Battalion, under Conte Luigi Maria Gatto, moved into Fort Ricasoli. The Provincial Battalions were reduced to a single battalion in Oct 1806.
On 16 May 1803, hostilities resumed between France and Britain. Medical officers who had been discharged on half-pay were immediately recalled to the service.
In Sept 1803, an additional assistant surgeon was allowed for infantry regiments with more than 500 men. The assistant surgeons were on the establishment of the regiment and were appointed by the commanding officers of the regiments.
On 8 July 1803, Vice Admiral Lord Horatio Nelson assumed command of the British Mediterranean Fleet. Regiments in Malta were placed in readiness to support Nelson in securing Sicily from the French.
Capt Alexander Ball RN who had arrived in Malta as Minister Plenipotentiary to the Order of St John resumed the duties of Civil Commissioner and suspended the evacuation of Malta. Ball administered Malta in accordance with his instructions that the island was to be managed in conformity with the Laws and Customs of the Maltese. To that aim he restored the Luogotenenti or village chiefs, who, under the Order of St John had looked after the affairs of the village. During his administration Ball inaugurated a number of public gardens.
Instructions to regimental surgeons for regulating the concerns of the sick and of the hospital – were published by Horse Guards in Sept 1803.
1. The regimental surgeon and assistant surgeon shall regularly visit the hospital at least every day.
2. The surgeon shall keep a book of admissions, discharges, and the cases of the patients in which the name of the disease, diet, and treatment are to be fully inserted, subject to the call of the Inspector General of Army Hospitals or Commanding officer of the regiment.
3. The inoculation of the cow pox is to be constantly practiced. Let every man who does not bear the mark of the small pox, either by inoculation or otherwise, be subject to the trial of the cow pox.
4. The bed stoppage drawn from men in hospital is fixed at 10 pence a day.
5. The wives and children of soldiers are allowed medicines from the medical chest but this indulgence is not to extend to any charge on the hospital fund.