After taking the British Minister Plenipotentiary, Anthony Merry and his suite, to the United States, Phaeton sailed to the Cape of Good Hope, for operations against the French on the Isle de France.

He then rejoined Cockburn again to serve as master's mate aboard Pompee, which sailed to the Caribbean in late 1808, and took part in the reduction of Martinique in early 1809,[2] during which Scott was slightly wounded.

Scott then took part in the Walcheren Campaign, commanding a gun-boat during the attack upon Flushing, and for his conduct he received a letter of thanks from Rear-Admiral Sir Richard Goodwin Keats, and on 16 November 1809 was appointed lieutenant aboard the sloop Fleche, Captain George Hewson.

In August 1812, Cockburn was promoted to rear-admiral and Scott followed him into his flagship Marlborough, which in November sailed to the coast of North America to take part in the War of 1812.

In 1814, now serving as first lieutenant of Albion, Scott took part in the storming two forts on the eastern shore of the Chesapeake (including the 25 June Raid on Chesconessex Creek),[4] in the destruction of Commodore Joshua Barney's Chesapeake Bay Flotilla on the Patuxent River, and served on shore as aide-de-camp to Rear Admiral Cockburn during the battle of Bladensburg, the burning of Washington, and at the failed attack on Baltimore.

[2] On 19 October 1814, Scott was promoted to commander, but received no ship until 4 May 1824 when he was appointed to the bomb vessel Meteor to take part in the demonstration before Algiers made by Vice-Admiral Sir Harry Burrard-Neale.

On 31 October 1839, he was appointed to command of the sixth-rate post ship Samarang off South America, and then on the East Indies and China Station, serving in the Second Opium War.

Before the first investment of Canton, he moved temporarily into the East India Company's iron-hulled steamer Nemesis, commanded by Captain William Hutcheon Hall, to force a passage up the Broadway river between Macao and Whampoa.