When the 1745 Rising began, Murray was appointed sheriff depute to Sir John Cope, government commander in Scotland but then joined the Jacobite army when it arrived in Perth on 3 September.

However, his support for the 1707 Union set him apart from the majority of Scottish Jacobites, and previous links with the government meant that many viewed him with suspicion: combined with a perceived arrogance and inability to accept advice, this reduced his military effectiveness.

They had three sons and two daughters who survived to adulthood; John, later 3rd Duke of Atholl (1729–1774), Amelia (1732–1777), James (1734–19 March 1794), later a Major-General in the British army, Charlotte (?–1773) and George (1741–1797), who became an admiral in the Royal Navy.

This was resurrected as part of the 1719 Rebellion, whose main component was a Spanish landing in South-West England; its objective was to capture Inverness, and enable a Swedish naval expeditionary force to disembark.

[9] This seemed to end hopes of a Stuart restoration; in a letter of 16 June 1719 to the Earl of Mar, Tullibardine concluded 'it bid fair to ruin the King's Interest and faithful subjects in these parts.

[11] Murray's activities over the next four years are obscure, but included attending the Académie royale des sciences de Paris and fighting a duel with fellow Jacobite exile Campbell of Glendaruel.

[13] After Charles landed on Eriskay in July 1745, accompanied by the now elderly and sick Tullibardine, Murray was appointed sheriff depute for Perthshire and advisor to the government commander Sir John Cope.

[14] His reasons remain obscure; at the time, he cited the government's "corruption and bribery" and "wars all entered into for and on account of the Electors of Hanover" as necessitating "a Revolution to secure our liberties".

[16] Accepting a pardon in 1725, swearing allegiance to George II in 1739 and taking a position under the same 'corrupt government' meant others viewed his actions as the opposite of virtuous and honest, including his eldest son.

'[19] Murray considered O'Sullivan's expectations of the Highland recruits unrealistic, including formal drill and enacting written orders, while the exiles viewed this as outdated.

[20] One of the exiles, Sir John MacDonald, wrote Murray's strategic vision was jeopardised by ignorance of tactical execution, an example being the failed night march before Culloden.

[22] One example was a furious argument with Charles prior to the Battle of Prestonpans; although his rejection of a frontal assault in favour of attacking Cope's left flank proved correct, it caused deep offence.

His opinion of Charles was widely shared; MacDonald of Sleat refused to join the rebellion as a result, while French envoy d’Éguilles later suggested a Scots Republic was preferable to a Stuart restoration.

O'Sullivan felt their army was too small to conquer England but lack of recruits and money made action imperative; Edinburgh had been 'devastated for 30 miles around' by Jacobite foragers and the prisoners taken at Prestonpans were released because they could not feed them.

He then resigned his command, ostensibly because Charles refused to rotate troops besieging the castle, but in reality because he was unhappy about serving under his fellow lieutenant-general, the well-liked but inexperienced Catholic Duke of Perth.

[32] Exhausted by a failed night march suggested by Murray in an attempt to surprise Cumberland's army, many of their troops missed the Battle of Culloden on 16 April, which ended in a decisive government victory.

'[35] This suggests the Hanoverians' greatest failing in his eyes was being foreign, an attribute shared by Charles, a young man brought up in Italy whose first language was French, and whose mother was Polish.