Promoted to commander on 22 June 1796, he appointed to command of the 16-gun sloop. In May 1797 he was sent by the Port Admiral at Sheerness to negotiate with the mutineers at the Nore, and also assisted in securing the dockyard from any attempt by the mutineers to capture it. Pylades was then stationed principally off the Dutch coast, where Mackenzie greatly distinguished himself.
In July 1797 he recaptured the Thetis, Ocean, John, and Swan.
In April and May 1798 he captured the fishing vessels Staadt Altona and De Hoop.
On 27 March 1799 he captured the Noyt Gedacht and Goode Hoop.
On 12 May 1799 Pylades and captured the Vrow Etje.
Pylades was part of a squadron led by Captain Frank Sotheron in the frigate, composed of the frigate, the brig-sloop, the sloops Ranger and, the hiredcuttersCourier, Fox and Diligent, and the hired luggerSpeculator, that captured six Dutch ships between March and May 1799. Pylades received a share of the prize money paid for three of them; Vinnern, Jonge Picter and Ferwagting, but after deductions for the cases of six other ships, Mackenzie's share came to only £31 13s 0d.
On 10 July 1799, he led an attack by boats near the island of Ameland, bringing out three valuable merchantmen, and burnt a galliot, loaded with ordnance stores.
Mackenzie's most notable action during this time took place on 11 August 1799, when Pylades, accompanied by the 14-gun sloop, under Captain James Boorder, and the 12-gun hired cutter Courier, under Lieutenant Thomas Searle, reinforced with men and boats from the frigates Latona and, were sent to recapture the, a former British gun-brig, which lay moored between the island of Schiermonnikoog and the mainland of Groningen. The Courier, faster and smaller than her companions, was sent ahead to engage the Crash, despite being heavily outgunned, with Courier mounting only twelve 4-pounder guns, while Crash was armed with eight 18-pounders, two 24-pounders and two 32-pounders, all carronades. Sailing into the wind in the narrow and shallow channel delayed the arrival of Pylades and Espiegle, however they eventually arrived to within pistol-shot of Crash, which surrendered after a determined resistance. At the same time the boats of Pylades, Latona and Juno pursued a large armed schooner, forcing her to run ashore to avoid capture, before capturing a schuyt. Lieutenant James Slade of the Latona was given command of Crash, and Lieutenant Salusbury Pryce Humphreys of Juno that of the schuyt, which Mackenzie armed with two 12-pounder carronades and named Undaunted. Two days later, on the afternoon of the 13th, the British returned to attack a shore battery of six guns on Schiermonnikoog, and the schooner Vengeance, armed with two long 24-pounders, four guns of smaller calibre, and 70 men, which was lying with a large row-boat, and several merchant vessels, near the island. Crash and Undaunted, accompanied by the launches of the Latona and Pylades, each mounting a 12-pounder carronade, and several smaller boats armed with swivels and muskets, all under the command of Lieutenant Slade, approached to attack. Unfortunately, Crash grounded too far out to aid to Lieutenant Humphreys in Undaunted, who steered towards the Vengeance, arriving alongside just after her crew had abandoned her. The strong tide, and the tumblehome of both ships prevented Humphreys jumping aboard, so he attempted to swim across with a rope, but was defeated by the strong current and was hauled back to the Undaunted. This was fortunate, for he had only just returned to his own ship when the Vengeance exploded, her crew having left a fuze burning in the magazine. In the meantime the boats had landed on Schiermonnikoog, captured the battery and spiked the guns. Assisted by Undaunted they then brought off two brass field pieces, the row-boat, and twelve schuyts. In 1847 the Admiralty authorised the issue to the surviving claimants of the Naval General Service Medal with clasp "Schiermonnikoog 12 Augt. 1799".
Frigate captain
Mackenzie was then present at the capture of the Dutch fleet of Vice-Admiral Samuel Story on 30 August 1799, and was promoted to post-captain on 2 September. He remained on half-pay until October 1801, when was appointed to the 28-gun, commanding her until March 1802, when the Treaty of Amiens brought a temporary peace. . At the renewal of the war in May 1803, Mackenzie was given command of the frigate, and was employed in the blockade of the enemy's coast into the following year. He then escorted vessels taking 10 troops of horse and 1,000 infantry to the West Indies, where he had several skirmishes with the enemy's batteries, and destroyed many vessels. On 25 January 1806, in the Mona Passage, Magicienne and the sloop Penguin captured the Spanish packet El Carmen after a chase lasting 12 hours. The Spaniard was pierced for 14 guns, but mounted only two, and had a crew of 18 men. Magicienne also formed part of the squadron under Sir John T. Duckworth at the Battle of San Domingo on 6 February 1806. Mackenzie was subsequently ordered to escort a convoy from Jamaica to England. Soon after leaving the Gulf of Mexico, a hurricane struck, sinking twenty vessels, and obliging him to sail for Bermuda to repair damage.
On 13 May 1820, Mackenzie was appointed to command of the frigate, and in January 1821 to the ship to serve on the coast of South America. He rounded Cape Horn into the Pacific a few months later, during the southern winter, to protect British interests and property during the Wars of Independence. Superb was stationed as a guard ship at Plymouth by mid-1822.
Death
Mackenzie died in November 1823 and was buried at Stoke, his funeral attended by over 300 sailors and Royal Marines. The event was controversial, as after his death a woman had emerged claiming to be Mackenzie's secret wife and laying claim to his inheritance. The local vicar, Mr. Ley, carried out an investigation and determined that the woman had once been a mistress of Captain Mackenzie. Upon the end of their relationship she had conducted a marriage with a shipwright named George Condy, who had posed as Captain Mackenzie. Condy was confronted about the accusations and committed suicide, while the woman was arrested for attempting to fraudulently lay claim to Mackenzie's military pension.
