Among the Essex's many prizes was the whale ship Georgiana, "which Captain Porter fitted as a cruiser, with sixteen guns, named the Essex Junior, and placed under the command of Lieutenant Downes who retained this place until the capture of the Essex and the conversion of the Essex Junior into a cartel, 28 March, 1814."
He was promoted to master commandant in 1813, and two years later commanded the brig Epervier, in the squadron employed against Algiers under Stephen Decatur. On 17 June, 1815 he, in concert with the rest of Decatur's squadron, captured the Algerine frigate Mashouda. Two days later the Epervier and three of the smaller vessels of the squadron captured the Algerine brig of war Estedio with twenty-two guns and 180 men off Cape Paios. After the conclusion of peace with Algiers, Decatur transferred Downes to his own ship, Guerriere.
Downes took command of the captured HMS Macedonian, now called the USS Macedonian in 1818 and set forth on a three-year show of power for America to South America and beyond. On this trip, he decided to use the ship for his own enrichment and became a banking ship, giving protection, passage and banking service to privateers, pirates and others. He took large amounts for his own private use. He took at least 2.6 million in specie during his trip. He so angered his associtates, whom he kept busy counting money under poor conditions, that one of his midshipmen, William Rodgers, resigned from the Navy after coming ashore from this three-year voyage. He cited not being able to "do what I joined this man's Navy to do. Not being able to serve my country but to simply be serving for the monetary good of Captain Downes". Captain Downes had so much specie aboard that he was able to bribe Lord Cochrane into allowing the Macedonian to pass Cochranes Blockade.
In February 1831, the American merchant ship arrived at the harbor of Kuala Batu on the Pedir coast of Sumatra to take on a cargo of pepper. A Malay boat arrived, but as the pepper was loaded the Malays, on signal, attacked the officers and crew. According to Owen Rutter's "Pirate Wind," every American on board was killed before the pirates ransacked the ship and took its cargo.
The captain however, had been on shore with four of his crew. He returned to the ship, fled and received help from other American ships also trading on the coast. They returned to Salem, the headquarters of much of America's trade with the East at that time, and also reported that the local chieftain denied any knowledge of the attack in his harbor.
President Andrew Jackson, along with many Americans, was outraged and vowed retribution. If there was a regular government that Downes could deal with, he was authorized to negotiate with it, if not, he was to "inflict chastisement" on any "band of lawless pirates" responsible for the atrocity. Downes, in command of the Potomac left New York harbor August 28, 1831 bound for Kuala Batu by way of the Cape of Good Hope and the Indian Ocean.
Early on 7 February, Downes sent a detachment of marines and three detachments of seamen (a total of 282 men) with orders to take four Malay forts along the coast. They divided into three parties, attacked the forts in a combination of hand-to-hand combat and bombardment from the ship's 30-pound cannons. In five hours, the forts were taken, reportedly with all 150 of the defenders, including the local chieftain, fighting to the death.
On 9 February the ship bombarded the village itself, which caught on fire. The action resulted in another 300 dead.
When Downes arrived at Valparaiso, Chile, Jeremiah N. Reynolds, an American explorer and author, joined the expedition as the commodore's private secretary for the trip and wrote a book about the experience Voyage of the United States Frigate Potomac (New York: Harper and Brothers, 1835).
Downes' sea service terminated with this cruise.
On returning home, Downes was severely criticized for his harsh actions, but Jackson supported him, saying the fighting would deter future aggression. Yet the action wasn't absolutely successful -- in August 1838 another American merchant ship, the Eclipse was attacked by 24 Malays who had been allowed on board.
Three ships in the United States Navy have been named USS Downes in honor of him.