While this dispute was going on Popham had resumed his career as a naval officer. He served with the army under the
Duke of York in
Flanders as "superintendent of Inland Navigation" and won his confidence. The protection of the duke was exercised with so much effect that Popham was promoted commander in 1794 and post captain in 1795. He was then engaged for several years in co-operating in a naval capacity with the troops of Great Britain and her allies. His bills for the repair of his ship at
Calcutta were the excuse for an attack on him and for charging him with the amount. It was just the time of the general reform of the dockyards, and there was much suspicion in the air. It was also the case that
Lord St. Vincent did not like Popham, and that
Benjamin Tucker (1762–1829), secretary to the admiralty, who had been the admiral's secretary, was his creature and sycophant. However, Popham was not the man to be snuffed out without an effort. He brought his case before Parliament, and was able to prove that there had been, if not deliberate dishonesty, at least the very grossest carelessness on the part of his assailants. In the spring of 1798 the Admiralty created the
Sea Fencibles, a force of coastal militia, following a plan by Popham. On 8 May 1798 Home Popham led an
expedition to Ostend to destroy the sluice gates of the Bruge canal. The expedition landed a contingent of 1,300 British Army soldiers under the command of Major General
Coote. The troops burnt some ships in the harbour before blowing up locks and gates on the canal. His force then surrounded had to surrender as adverse winds prevented their re-embarkation. It was during this period perhaps in captivity, before being returned home that Popham began work on a standard signal instructions handbook for the Royal Navy. Ship to ship communication was very haphazard: a fleet system that protected vulnerable frigates on station was essential to save time and material. The global character of the navy required linking to larger fleet formations. During the 1799
Anglo-Russian invasion of Holland, Popham's gunboats played an important role in assisting
York's army in suppressing the French at
Krabbendam and
Alkmaar. During service on in the
Battle of Copenhagen Popham tested his telegraphic equipment. He acted as liaison officer to the Danish Court off station from Elsinore. Popham was under the direction of Admiral Archibald Dickson when he devised the two or three flag hoist, in which each sign was a number, and each combination a different state of readiness. The vocabulary was limited and totally nautical, apposite to a direct command. At Copenhagen boats could be sent ashore, but were unnecessary using only flag signals. Popham was deeply encouraged by Lord Spencer, 1st Lord of the Admiralty who advised publication of the signal books. The new signals were immensely useful to Nelson at Trafalgar in developing navy tactics in secret. Popham proved McArthur, his critic and rival, wrong; Popham's books were printed several times after the battle.
Red Sea expedition In early 1801 Popham brought out to the Cape of Good Hope several regiments. He then embarked the
22nd and
61st Regiments of Foot and the garrison on his transports and was expected on 28 February to leave on a secret expedition. At the time the speculation was that he would sail to attack the Spanish colonies in the
Río de la Plata. Instead, Popham sailed to the
Red Sea to support
General Baird's expedition to Egypt to help General
Ralph Abercromby expel the
French there. On 23 May 1801, he drew 6,000 Spanish dollars for His Majesty's ships on the expedition from the treasury on
Cuvera while she was in the
Judda roads. On 14 June 1802 the transport
Calcutta wrecked on the Egyptian coast in the Red Sea. She was carrying 331 men of the
80th Regiment of Foot and 79 native Indian followers. arrived the next day, as did two transports. Only
Romney was able to get her boats out but they were able to rescue and deliver to the shore all but seven men who had died in an early attempt to reach shore. Popham, in
Romney, left to salvage anything that could be salvaged and then sailed to Suez from whence he dispatched to pick up the troops on the 15th and carry them back to India.
Río de la Plata expedition Commissioned by prime minister
Pitt in 1805 to study the military plans being proposed by Venezuelan revolutionary
Francisco de Miranda to the British Government, Popham then persuaded the authorities that, as the Spanish Colonies were discontented, it would be easy to promote a rising in
Buenos Aires. he led the first of the
British invasions of the River Plate, transporting General Beresford's brigade of 1,500 men with his squadron. Over 100 men died from sickness leaving 1,400 weakened soldiers when they arrived; but the Spanish colonists, though discontented, were not disposed to accept British rule. They rose up against the soldiers who had landed, and took them prisoners. Popham's ships bombarded the taken citadel, but he was recalled, and censured by a
court martial for leaving his station. In spite of his embarrassment the City of London presented him with a sword of honour for his endeavours to "open new markets", and the sentence did him limited harm.
From Spain to North America Station In 1806 Popham was appointed a groom of the bedchamber to the Duke of Gloucester. With a collaborator, John Goodhew, he published ''A General Code of Signals for the use of His Majesty's Navy'', in which there were only twelve flags doubled backed to make twenty-four flags were used and no numbers. Variation was provided by a pendant, and changes were made to the key to maintain secrecy. But Popham's original system offered the Admiralty a huge variety of signals to be sent interpolated by tables with places marked around the world. Popham's was both complex and sophisticated for the time, but limited by a bifurcated alphabet. In 1807
Lord Gambier appointed him captain of the fleet for the
Second Copenhagen Expedition. In 1812 and 1813 he was stationed on the northern coast of Spain where he worked with the Spanish
guerrillas to successfully harry the French troops and assault French fortresses on the
Basque coast while
Wellington was advancing through Spain. This was capped off with a personal gift from Prince Regent in the
Knight Commander of the Royal Guelphic Order in 1818. ==Parliament==