Jones was promoted to the rank of captain on 4 September 1782, and took command of the 74-gun HMS Hero, commanding her in the 1783 Battle of Cuddalore under Admiral Sir Edward Hughes. He was one of the first British officers engaged in the French Revolutionary Wars, commanding HMS Andromache in 1793, then the 64-gun HMS Trident. In 1796, Jones took command of the 74-gun HMS Defiance. Defiance had already seen a mutiny in 1795, which had been ended by Captain William Bligh. Bligh had taken 200 troops on board his Calcutta, and bringing them alongside Defiance had been enough to end the mutiny without a boarding. The crew mutinied again while under Jones's command, as part of the Channel mutinies in 1797. In 1798, during the Irish Rebellion, Defiance was in Portsmouth. A plot was discovered amongst Catholic crewmen, who had taken an oath to seize control of the ship and take her to Brest under a green ensign with a harp on it, killing all the officers except the captain. Twenty-five men were court-martialled aboard HMS Gladiator in a hearing which began on 9 September under Captain Holloway. Jones conducted the prosecution, and on 13 September the court adjourned to deliberate. The following day, 14 September, all but one were found guilty. Holloway pronounced them traitors, and Judge Advocate General Greetham read the sentences. Nineteen were sentenced to death by hanging aboard a ship, though eight were recommended for mercy, to be transported for life. Two men were sentenced to 200 lashes and 12 months solitary imprisonment, two to 100 lashes and six months imprisonment, and one to 12 months imprisonment. A government order was received in Portsmouth on 26 September, setting the following day for execution of 11 men. The hangings took place as ordered on Thursday 27 September. At 9am on board HMS St George off Spithead, seven men were "launched into eternity". At 11:15 am, the remaining four were hanged on board HMS Resolution, in Portsmouth harbour. All but one of the condemned men maintained their innocence to the end, and The Observer newspaper reported that "every means was adopted to make the execution on Thursday as awful and impressive as possible". Jones later commanded the three-deckers HMS Atlas and HMS Queen, but did not hold a command after the 1802 Treaty of Amiens temporarily ended hostilities between the French First Republic and the United Kingdom. He was promoted to rear admiral in 1802, vice admiral in 1809, and full admiral in 1819. He died on 8 November 1835 in Maidstone.