In the West Indies
During operations in May 1796 against Saint Lucia, Ussher, who had been appointed acting-lieutenant of the Minotaur (74), under Captain Thomas Louis, was employed on shore in command of a party of seamen attached to the army under Sir Ralph Abercromby.
He was promoted to lieutenant on 17 July, and following the surrender of the island, was appointed to the 18-gun brig Pelican, serving under a series of captains; John Clarke Searle, Thomas Harvey, Edward Kittoe, John Gascoyne, John Hamstead, Christopher Laroche, and Robert Philpot.
On 23 September 1796, while under the command of Captain Searle, the Pelican, with only 97 men on board, fought off the 32-gun Médée near La Désirade, in a close action. The Médée sustained losses of 33 men killed and wounded, while the Pelican, although her sails and rigging were cut to pieces, had only one man slightly wounded. Later the same day Pelican retook the Alcyon, a British army victualler which had been captured by the Médée. Ussher was given command of her, but on the 24th the Alcyon was recaptured by the French close to Guadeloupe; and he was for a short time detained as a prisoner.
Ussher rejoined the Pelican on 27 September 1797, and took part, while the ship was under the temporary command of Lieutenant Thomas White, in the destruction of Le Trompeur, a French privateer of 16 guns and 160 men, not far from Santo Domingo. The vessel was engaged by Pelican for 35 minutes before attempting to escape, but was overtaken and sunk. Only 60 of her crew were saved.
On 2 April 1798 Ussher was sent out in command of two boats containing 14 men to search various creeks in Cumberland Harbour and St. Jago de Cuba for a privateer which had been raiding the coast of Jamaica. On the 4th Ussher landed in a sandy bay near St. Jago to rest when his men were suddenly attacked by a force of 60 to 70 soldiers. Under a volley of musket fire Ussher, though slightly wounded, succeeded in reaching a boat and returned fire with a swivel loaded with 200 musket-balls. The enemy fled; and the British, having 2 killed and 10 wounded, also retired.
The next day, 5 April, while reconnoitring the mouth of the river Augustine, near Cumberland Harbour, he observed the French privateer schooner, Le Moulin a Cafe, of 7 guns and 83 men, which was lying across the stream, with her bows apparently aground and most of her crew on shore. He attempted to capture her, but the crew boarded as he approached, and using hawsers hauled the schooner into the river channel. Ussher called on them to surrender, and received a broadside in reply. He attempted to board under cover of the smoke, anticipating reinforcements from the Pelican, but was shot through the right thigh. Seeing that the attempt was a failure he ordered his men to retreat, then fainted from loss of blood. On recovering he found himself for a second time in the hands of the French.
For several months after his return to the Pelican, his wound meant that Ussher was on crutches, but despite this in January 1799 he volunteered to take Pelican's cutter and 12 men in an attack on another privateer, La Trompeuse, of 5 guns and about 70 men, lying in the Artibonite River, in the west of Santo Domingo. The privateer was boarded, and found to be fast aground, so was destroyed. This was only one of more than 20 boat engagements in which Ussher was present while aboard the Pelican.
In May 1799 Ussher joined the 36-gun frigate Trent, under Captain Robert Waller Otway. On 7 June he boarded a schooner moored in Aguada Bay, Puerto Rico, under the guns of a large battery. Having towed the prize out while under fire, he then returned and also brought out a felucca.
In July 1799 he commanded the boats in the capture of a Spanish vessel at Laguira having entered the port in an attempt to retake the British frigate Hermione, which unfortunately had sailed a few days previously. He subsequently captured a felucca found lying under a small battery on the north side of Puerto Rico.
In September 1800 Trent returned to England with Admiral Sir Hyde Parker aboard, and Ussher, still suffering from the effects of his wounds, was obliged to go on to half-pay. Although the College of Surgeons assessed his injuries as equal to the loss of a limb, he was unable to procure any compensation. Ussher applied for employment in June 1801, against the advice of his doctors, and was appointed to command the cutter Nox, stationed off Weymouth in attendance upon the King, where he remained four months.