In April 1809 Napier took part in the capture of Martinique, and subsequently distinguished himself in the pursuit of three escaping French ships of the line, handling the small Recruit so well that their flagship, the Hautpoult (74), was captured. As a result was promoted acting post captain and briefly given the command of the captured 74. His rank was confirmed, but he was put on half-pay, when he came home as temporary captain of HMS Jason (32) escorting a convoy. He spent some time at the University of Edinburgh, and then went to Portugal to visit his three cousins, (all colonels serving in Wellington's army, and one of whom was Charles James Napier, the future conqueror of Sind). He took part in the Battle of Buçaco, during which he saved his cousin Charles's life and was himself wounded. In 1811, he was appointed captain of the frigate HMS Thames (32) and served in the Mediterranean, disrupting enemy shipping. Among his principal exploits was the capture of the island of Ponza, which was a haven for corsairs. In 1813 he moved to command the frigate HMS Euryalus (36), operating mainly off the French and Spanish Mediterranean coast.
He next distinguished himself in the attack on the city of Baltimore by a British army and 16 warships, 12–14 September 1814, under Admiral Cochrane. Euryalus was involved in the bombardment of Fort McHenry that began early in the morning of the 13th. The critical period of the attack developed shortly after midnight when a picked British force in longboats under Napier’s command penetrated the branch of the river to the west of the fort with the intention of storming it from the flank. Before they could land, however, they were detected and subjected to a withering fire from the guns of Fort McHenry and two smaller forts. The British fought back strongly with cannon and rockets. (Watching the battle from a safe distance, Francis Scott Key was inspired to compose 'The Star-Spangled Banner’.) Eventually American fire power prevailed; Napier was compelled to retire to the warships, and Cochrane’s fleet withdrew on the morning of the 14th.
Euryalus proceeded to Halifax, Nova Scotia for refit and then took part in the ongoing blockade of the eastern seaboard of the USA. Bored by such duties, Napier issued a challenge to the American frigate Constellation, which was lying at Norfolk, Virginia, to come out and fight a single-ship duel. The challenge was accepted and due arrangements were made ‘in the most gentlemanly fashion’, but Euryalus was made part of the squadron that Admiral Cochrane took to Florida and Louisiana in December 1814 in the operations that climaxed in the Battle of New Orleans on 8 January 1815, and before she could return to fulfil her engagement with Constellation news of the peace treaty of Ghent reached the USA.
With Napoleon's escape from Elba and brief return to power, (the 'Hundred Days'), Euryalus returned to Britain. Napier's last mission of the Napoleonic wars was to land troops at the mouth of the River Scheldt to guard against the French advance into Belgium.
At the beginning of 1829 he was appointed to command the frigate Galatea (42), and was given permission to fit her with paddles of his own design, worked by winches on the main deck, and carried out trials with them that successfully proved that ships could travel independently of the wind. This innovation was not adopted by the Admiralty. At the start of Portugal's Liberal Wars in 1832 Napier was at the Azores, which were the only part of Portuguese territory still held for Queen Maria II of Portugal against the usurpation of her uncle, the absolutist Dom Miguel. He so much impressed the constitutional leaders, especially the Count de Vila Flor (better known by his later title of Duke of Terceira), that they begged him to take command of their small fleet. He accepted in February 1833 after Galatea was paid off. Sailing to Portugal with troop reinforcements and using the incognito of 'Carlos da Ponza', he arrived in Oporto, where Queen Maria's father Dom Pedro, ex-Emperor of Brazil, and the Liberal forces were being besieged by Miguel's armies. He assumed command of the Liberal fleet, succeeding its previous British commander George Rose Sartorius. With it he then transported the Liberal army to the Algarve to open a second front in the south of the country, and on his return voyage destroyed the much larger Miguelite fleet in the Battle of Cape St Vincent on 5 July 1833. These two strokes enabled the Liberals to capture Lisbon, which was abandoned by the Miguelites, though Napier's squadron was now ravaged by cholera. On the demand of France he was struck off the English navy list. On the other hand Dom Pedro appointed him Admiral of the Portuguese Navy on 10 July; and his victory, with a fleet largely manned by British seamen, was viewed in Britain as a credit to the Royal Navy, though it greatly annoyed King William IV, who disliked both Napier and Dom Pedro. Continuing his Portuguese services, he commanded land forces in the successful defence of Lisbon, September 1833, when he was made Grand Commander of the Tower and Sword, and Count of the Cape of Saint Vincent in the Peerage of Portugal. In 1834, with a small army made up largely of British sailors, he reconquered the Minho region for the constitutional cause. After the final defeat of Miguel and the death of Dom Pedro shortly afterwards, Napier found himself frustrated in his attempts to reform the naval administration of Portugal and returned to England. His departure was followed by a vote of thanks to him in both houses of the restored Portuguese parliament. He occupied himself until 1836 with writing a history of the Portuguese War and his own part in it.
The Egyptians abandoned Beirut on 3 October. While preparing to attack them at Nahr-el-Kelb, Napier was ordered to relinquish command of the army to withdraw and hand over the land forces to the now recovered Brigadier-General Smith. To do so would have meant giving up the tactical initiative, and Napier accordingly disobeyed the order and continued with the attack against Ibrahim’s army. The ensuing Battle of Nahr-el-Kelb, or Kelbson, on 10 October, was a hard-fought victory, one of the very few land battles won by a naval officer. By the end of the month the only coastal position still held by the Egyptians was Acre, which Stopford was instructed to recapture. On 3 November the Mediterranean Fleet, with its Turkish and Austrian allies, moved into position against the western and southern sides of the town. The fire of the ships (48,000 rounds in all) was devastatingly accurate. A shell penetrated the main magazine in the south of the city, which exploded killing 1,100 men. That night Acre was occupied. British losses were only 18 men killed and 41 wounded. During the action, Napier had manouvred independently against Stopford’s orders and his division, by accident and mutual misunderstandings, left a space in the fleet’s deployment, not that this affected the outcome. Some captains wanted Napier to be court-martialled for insubordination, but Stopford did not push the issue.
The rapid collapse of Mehmet Ali’s power, with the prospect of bloody chaos in Egypt, was not part of the Allies’ plan, and Stopford sent Napier to command the squadron at Alexandria and to observe the situation. Here, acting once again on his own initiative, he appeared before the city on 25 November and enforced a blockade. Then without reference to his Admiral or the British government he personally negotiated a peace with Mehmet Ali, guaranteeing him and his heirs the sovereignty of Egypt, and pledging to evacuate Ibrahim’s beleauguered army back to Alexandria, if Mehmet in turn renounced all claims to Syria, submitted to the Sultan and returned the Ottoman fleet. 'I do not know if I have done right in settling the eastern question', Napier wrote to Lord Minto, the First Lord of the Admiralty. Stopford repudiated the arrangement immediately when he had heard the news, the Sultan and the British ambassador were furious, and several of the Allied powers declared it void. Nevertheless the formal treaty later concluded and confirmed on 27 November was essentially a ratification of Napier’s original, and he was congratulated by his friend Lord Palmerston. (Mehemet’s last heir, King Farouk, was still ruling Egypt in 1952.)
Napier continued to be interested in warship design and was responsible for the design of the paddle-frigate HMS Sidon launched in May 1846. In the same year he lost his parliamentary seat but was promoted Rear-Admiral of the Blue on 9 November. In May 1847 he was appointed to the command of the Channel Fleet, hoisting his flag in HMS St Vincent (120). By this time he was perhaps the naval personality most famous to the general public: his level of everyday name-recognition is shown by the passing allusion in William Makepeace Thackeray's famous humorous ballad Little Billee ("the British fleet a-riding at anchor / with Admiral Napier, K.C.B.").
The Channel Fleet was sometimes a sinecure, but this was by no means the case during Napier’s period of command. The fleet’s area of operations was not just the English Channel but more or less throughout what in the 20th century would be called the Western Approaches. Portugal was in the closing stages of its ‘little’ civil war, the Patuleia, and British interests in that country needed protecting. Ireland, in the aftermath of the Potato Famine, was feared to be near insurrection. Moreover there were considerations of experiment and training with new ships, made necessary by the rapid technological advances such as screw propulsion. During 1848, the fleet was mainly off the coast of Ireland, where the political situation dictated that Napier show the flag and train for the eventuality of transporting and landing soldiers on practically any part of the Irish coast. In December he took the Channel Fleet further than it had ever operated before, when it was sent to Gibraltar and then onto the Moroccan coast, with the purpose of curbing the activities of Riff pirates. He compelled the Emperor of Morocco, Muley Abderrahman, to grant compensation for the injuries he had inflicted on British commerce.
Napier returned to Britain in April 1849 and was ordered to strike his flag. His disappointment that his expected three years term had been cut short led to bitter letters to The Times criticising the Admiralty’s policy. When he applied for the vacant Mediterranean command, the Government and Admiralty agreed that he could not be trusted and he was rejected, Rear-Admiral Sir James Dundas being appointed instead. This led Napier to write more angry letters to the newspapers and directly to Lord John Russell claiming that he had been defrauded of his just rights. He unsuccessfully contested the parliamentary seat for the Borough of Lambeth. On 28 May 1853 he was promoted to Vice-Admiral of the Blue.
On the outbreak of the Russian War, better known as the Crimean War, he received the command of the largest fleet which the Royal Navy had assembled since the Napoleonic Wars, destined to act in the Baltic Sea. This was not without misgivings on the part of the Admiralty, but he was the most senior and experienced officer available. Napier hoisted his flag in February 1854 in the steam ship of the line HMS Duke of Wellington (131), his subordinate commanders being the Rear-Admirals Armar Lowry Corry, second in command, Henry Ducie Chads, third in command, and James Hanway Plumridge, commanding the scouting forces. They were all elderly men, at most a year or so younger than Napier himself. Napier's force, which was augmented in June by a French fleet sent by Napoleon III, though impressive on paper, was radically unsuited to operations in the Baltic and he was hampered by contradictory sets of orders from the Admiralty. Nevertheless he successfully blockaded all the Russian ports, sufficiently overawed the Russian Baltic Fleet that it never stirred from its moorings, and carried out many bombardment operations as far as the northernmost point of the Gulf of Finland. During the campaign the first ever Victoria Cross was won by a Midshipman of the gunboat HMS Hecla who threw a Russian explosive shell overboard before it could detonate. During the campaign Rear-Admiral Corry was invalided home because of poor health; he was replaced by Commodore (later Rear-Admiral) Henry Byam Martin. The major success of the campaign was the capture and destruction, in a near-perfect combined operation by French and British soldiers and sailors, of the Russian fortress of Bomarsund on the Aland Islands, which were temporarily liberated from Russian rule and which Napier offered to Sweden (they were declined). But he refused to attack the great naval bases at Sveaborg (often misquoted as the "Gibraltar of the north") and Kronstadt, which observation had established were probably impregnable without shallow-draught bomb vessels which he did not have; and a great outcry (led by the Times newspaper) was raised against him for his apparent lack of determination. (His inaction was thoroughly justified by the sequel: in 1855 a better-equipped Anglo-French fleet did bombard Sveaborg, but despite an enormous expenditure of ammunition caused the fortress only trifling structural damage.) Napier felt he was continually being second-guessed by the Admiralty, and especially by the First Lord of the Admiralty, Sir James Graham. In fact the Naval Lords were reacting to adverse press coverage and unwilling to accept the assessment of the commander on the spot, and relations between them deteriorated as his ships maintained the blockade in atrocious weather, quite unable to storm or destroy impregnable Russian fortresses into the bargain. Never one to mince his words or submit to what he felt to be unmerited criticism, Napier's 'disrespectful' tone in his despatches, which the Admiralty complained of, sealed his professional fate.
The Admiralty attempted to make Napier a scapegoat for the perceived failure of the campaign (which, within the limits of the possible, had been rather successful) and suborned several captains to testify to their lack of confidence in him, his timidity, his age, his lack of understanding of steam tactics, and his heavy drinking. Nevertheless some of the leading seamen in the fleet, such as Captain (later Admiral) Sir Bartholomew Sulivan, maintained along with him that Napier's strategy had been wise and the faults lay with the Admiralty themselves.
After the war the Russians testified that, knowing Napier's reputation, their main hope had been of his making a foolhardy attack on their fleet under the guns of Kronstadt, where they were confident he would have come to grief. Napier was elected MP for Southwark in February 1855, and carried his dispute with the Admiralty to the floor of the House of Commons. He was never given another command. He continued to campaign vigorously for the improvement of the way common seamen were treated during and after service, and maintained his parliamentary seat, though broken in health, until his death on the 6 November 1860. His tomb is in the churchyard of All Saints, Catherington in Hampshire. The ships of the Portuguese Navy went into eight days of mourning for their former commander.
Just before his death he was hoping to persuade Giuseppe Garibaldi to acquire a fleet for the liberation of Italy, which he would command.