Following Bligh’s overthrow Johnston had notified his superior officer, Colonel William Paterson, who was in Tasmania establishing a settlement at Port Dalrymple (now Launceston) of events. Paterson was reluctant to get involved until clear orders arrived from England. When he learned that Lieutenant-Colonel Joseph Foveaux was returning to Sydney with orders to become acting Lieutenant-Governor, Paterson left Foveaux to deal with the prevailing situation. He arrived on 28 July and immediately took over the colony but he left Bligh under house arrest. He felt that Bligh’s behaviour had been insufferable but, personal feelings apart, restoring the deposed governor scarcely practicable since the NSW Corps would certainly have opposed such a move. He at once took secure hold of the reins of government, dispensing with the services of John Macarthur who as ‘Secretary’ had been the power behind Johnston. The broad outlines of his policy were influenced by the same desire for cheap and efficient government that had guided his work on Norfolk Island and he sought to make his administration acceptable to London by pursuing objectives it had long favoured. He attacked the liquor trade and tried to reduce expenditure, reform the administration of the commissariat and improve public works turning his attention to improving the colony’s roads, bridges and public buildings. Efforts were made to encourage the raising of beef and mutton, while he tried to persuade smallholders to breed additional swine, thereby providing an outlet for their surplus maize. His land policy was moderate and he made few grants, though he did alienate some town land that was properly available only for lease.
Annandale House, on the estate of Lt. Col. George Johnston
Little exception can be taken to these aspects of Foveaux’s rule. However, his treatment of the pro-Bligh faction was severe and sometimes unfair. The troublesome Bligh refused to depart and was bitterly criticised in Foveaux’s dispatches. George Suttor and a group of his associates were imprisoned for challenging his authority by refusing to attend a muster. He disallowed Robert Campbell’s contract with David Collins to import cattle to the Derwent, criticised Campbell’s assistance to Bligh and accused Campbell and John Palmer of benefiting greatly from the liquor trade. It has been argued that advice from officers who were jealous of Campbell’s trading position underlay these moves and that Foveaux, acting as their tool, sought to destroy the merchant. If true, it was a serious flaw in what was quite an enterprising administration.
When there was still no word from England, he summoned Paterson to Sydney on 9 January 1809 to sort out matters. Paterson sent Johnston and Macarthur to England for trial and confined Bligh to the barracks until he signed a contract agreeing to return to England. His opinion of Bligh was not high and he certainly regarded Bligh as culpable in causing the rebellion
He bore the most rancorous ill-will to every Officer and Inhabitant who he conceived could possibly in the remotest manner interfere with a matured plan of exercising the high command with which he was honoured in the purposes of gratifying his insatiably tyrannic Disposition and advancing his pecuniary interest.
Paterson, whose health was failing, then retired to Government House at Parramatta and left Foveaux to run the colony. In January 1809, Bligh was given the control of HMS Porpoise on condition that he returned to England. However, Bligh sailed to Hobart in late March seeking the support of the Tasmanian Lieutenant-Governor David Collins to retake control of the colony. Collins did not support him and on Paterson’s orders Bligh remained cut off on board the Porpoise moored in Hobart until January 1810. 
It was two years before the rebellion was finally quenched. The threat of Napoleon was a more important threat as his armies trampled across Italy and Spain and Britain also became involved in an unhelpful conflict with the United States that eventually led to war in 1812. After considerable delay, the Colonial Office decided that sending naval governors to rule the colony was untenable. Instead the NSW Corps, now known as the 102nd Regiment of Foot, was to be recalled to England and replaced with the 73rd Regiment of Foot, whose commanding officer would take over as Governor. Bligh was to be reinstated for 24 hours and then recalled to England. Johnston was to be sent to England for court martial and Macarthur tried in Sydney though both were already on their way to London. Major-General Lachlan Macquarie was put in charge of the mission after Major-General Miles Nightingall fell ill before departure. Macquarie took over as Governor with an elaborate ceremony on 1 January 1810.
Portrait of Lachlan Macquarie attributed to John Opie
Governor Macquarie reinstated all the officials who had been sacked by Johnston and Macarthur and cancelled all land and stock grants that had been made since Bligh’s deposition, though to calm things down he made grants that he thought appropriate and prevented any revenge. When Bligh received the news of Macquarie’s arrival, he sailed from Hobart to Sydney, arriving on 17 January 1810 to collect evidence for the forthcoming court martial of Major George Johnston. He departed for the trial in England on 12 May aboard the Hindostan, with recalled NSW Corps soldiers and witnesses including Atkins and Paterson, who died en route, for the trial against Johnston arriving on 25 October 1810. Mary Putland, recently remarried to Lieutenant-Colonel Maurice O’Connell remained in Sydney. Macquarie investigated the mutiny and reported finding no evidence that the insurrection resulted from any direct fault on Bligh’s part. Nor did he attribute the blame to any incident in the prolonged power struggle between the naval ‘Captain-General and Governor-in-Chief’ and the military force under his orders. In May 1810, Macquarie wrote to the Secretary of State in London that it was
...extremely difficult to form a just Judgement on this delicate and mysterious subject... in justice to Governor Bligh...I have not been able to discover any Act of his which could in any degree form an excuse for, or in any way warrant, the violence and Mutinous Proceeding pursued against him.
Given that he did not respect Blight and regarded him as a ‘most unsatisfactory Man to transact business with’, Macquarie’s statement appears unbiased. However, he refrained from commenting possibly deliberately as he had served with George Johnston in North America in 1777, on who, or what set of circumstances was responsible for the mutiny.
The ambiguity in this investigation was perpetuated in the subsequent court martial in England. On 3 April 1811, the newly appointed Prince Regent ordered the court martial of Johnston and on 7 May 1811, fifteen high-ranking officers and Judge Advocate General convened a court martial. The trial lasted 13 days, with 22 witnesses plus Bligh for Crown and 18 witnesses for Johnston. Having informally heard arguments from both sides, the government authorities in England were not impressed by either Macarthur’s or Johnston’s accusations against Bligh or by Bligh’s ill-tempered letters accusing key figures in the colony of unacceptable conduct. Against the patent fact of mutiny was set nothing more substantial than the governor’s temper, and unproven and irrelevant allegations of cowardice at the time of the arrest. On 6 June, Johnston was found guilty and cashiered from the military ‘for suffering to be led by Macarthur’, the lowest penalty possible. His barrister, John Adolphus who held the view that Johnston was a misled man, wrote after the trial
I always considered and indeed understood that the parties who led you into your present most unpleasant and unfortunate situation, would, at least, have taken off your shoulders the expense of the present prosecution, but as you refer in your letter to the smallness of your means, I beg you will consider me as entirely satisfied.
A similar note was struck by Johnston himself when he wrote in June 1820
Every person that promised [at the time of the deposition of Bligh to support me with their lives and fortunes] has risen upon my ruin. I alone am the sufferer, having lost my commission, and upwards of 6000 pounds for conceding to their requests. 
He was then able to return as a free citizen to Annandale his estate in Sydney.
Legal opinion was that none of the civilians involved could be tried for treason in England. Macquarie received instructions from Lord Castlereagh that ‘as Gov'r Bligh has represented that Mr McArthur has been the leading Promoter and Instigator of the mutinous Measures...you will, if Examinations be sworn against him...have him arrested thereupon and brought to Trial before the Criminal Court of the Settlement’. Macarthur’s obvious course was to remain in England and exert every influence to have this obstacle removed. Because of the uncertainty of his position he toyed with the idea of taking ‘a small Farm of about a Hundred a Year’ to help to balance his living expenses. At the same time he tried to resolve the problem of returning to NSW at personal risk and the alternative of withdrawing his family from ‘plenty and affluence’ in the colony to a life of ‘pinching penury’ in England. He became increasingly convinced that unless their colonial property would yield the £1,600 a year necessary to support the family and educate and establish his sons, he would have to return. Initially, none of Macarthur’s efforts in England clarified his position and it was not until early in 1817 that he received permission to return to NSW on condition that he should not become involved in public affairs. Exile itself was some sort of punishment.
Bligh’s promotion to Rear Admiral was delayed until the end of Johnston’s trial. Afterward it was backdated to 31 July 1810 and Bligh took up a position that had been kept for him. He continued his naval career in the admiralty in unspectacular fashion and died in 1817. Macquarie had been impressed with Foveaux’s administration. He put Foveaux’s name forward to succeed Collins as Lieutenant-Governor of VDL because he could think of no one more fitting and considered that he could not have acted otherwise with regard to Bligh. However, when Foveaux returned to England in 1810, he narrowly escaped court-martial for assenting to Bligh being deposed and imprisoned and Macquarie’s recommendation was ignored. Foveaux was taken back into active service and given command of a light regiment in 1811 and pursued an uneventful military career after that, rising to the rank of Lieutenant-General.
 Macmillan, David S., ‘Paterson, William (1755-1810)’, ADB, Vol. 2, pp. 317-319. Johnston’s letter is lost but Paterson’s reply on 12 March 1808 is printed in HRNSW, Vol. 6, pp. 536-538.
 Paterson to Castlereagh, 12 March 1808, HRNSW, Vol. 6, pp. 538-539. Bligh to Paterson, 8 August 1808, HRA, Series I, Vol. 6, pp. 601-601 was the first direct contact between Bligh and Paterson since the coup in which Bligh asked Paterson ‘to use your utmost endeavours to suppress this Mutiny of the Corps under your command, that I may proceed in the Government of the Colony according to the powers delegated to me by our Gracious Sovereign.’
 Ibid, Whitaker, Anne-Maree, Joseph Foveaux: Power and Patronage in Early New South Wales, pp. 103-116 deals with his months in charge. See also, Fletcher, B.H., ‘Foveaux, Joseph (1767-1846)’, ADB, Vol. 1, pp. 407-409.
 Bligh appealed to Foveaux to be reinstated: Bligh to Foveaux, 29 July 1808, HRNSW, Vol. 6, p. 713 but Foveaux refused to interfere. His justification can be found in Foveaux to Castlereagh, 4 September 1808, HRNSW, Vol. 6, pp. 728-735 and HRA, Series I, Vol. 6, pp. 623-631.
 This was particularly evident in a private letter from Foveaux to Under-Secretary Chapman (?), 10 September 1808, HRNSW, Vol. 6, pp. 749-754 and in Foveaux to Under-Secretary Cooke, 21 October 1808, pp. 783-784 where he suggested that Bligh was conspiring with settlers to support his restoration.
 Parsons, Vivienne, ‘Suttor, George (1774-1859)’, ADB, Vol. 2, pp. 498-500. Suttor was a firm supporter of Bligh and a leader among the settlers. In May 1808, he was instrumental in drawing up an address of welcome to Paterson, anticipating his arrival in Sydney and asking him to take action against the rebels; but as Paterson did not come it was not presented. In November, Suttor drew up another petition to be sent to the Colonial Office and with Martin Mason was chosen for a mission to London to explain the abuses in the colony and ask for the reinstatement of Bligh: Settlers’ Petition to Castlereagh, 4 November 1808, HRNSW, Vol. 6, pp. 802-804. In the meantime, however, Suttor was imprisoned for six months for failing to attend Foveaux’s general muster and for impugning his authority. In 1810, Bligh took Suttor with him in the Hindostan as a witness against the rebel leader, Colonel George Johnston.
 Steven, Margaret, ‘Campbell, Robert (1769-1846)’, ADB, Vol. 1, pp. 202-206. During the events that culminated in the deposition of Bligh, Campbell publicly and privately supported the governor’s attempts at reform, convinced that it was his liberalising economic measures that had goaded his opponents into open rebellion. In Campbell’s opinion Bligh ‘wished to administer justice to all ranks of people’. This exposed him to the hostility of the rebels and this had such adverse effects on his business interests that he claimed he was never fully able to repair the damage. When Bligh was deposed, Campbell was put under military arrest and subsequently was dismissed as treasurer, Naval Officer and collector of taxes. On the grounds that he was suspected of trying to establish a trading monopoly in collusion with Bligh, the rebel faction supervised the activities of Campbell & Co., supporting without investigation any damaging allegations concerning irregularities in their trade. In June 1809, Campbell was tried for disobedience in refusing to officiate as coroner. He argued that as he had been charged officially with certain offences he deemed himself incompetent to hold any civil position until such charges had been disproved; but the court, whose authority Campbell refused to acknowledge, found him guilty and fined him £50. Although his business partner and his brother-in-law, Commissary John Palmer, were both gaoled by the rebels, Campbell openly remained a supporter of their victims and a focus for Bligh’s allies. In January 1810, he was one of the first of those reinstated in their former offices by Macquarie. On 12 May Campbell, with his family, sailed unwillingly for England in the Hindostan to appear as a witness for Bligh at Lieutenant-Colonel George Johnston’s trial.
 In poor health and drinking heavily, Paterson was a weak ruler. He spent most of the year at Parramatta as an invalid and the clique that had overthrown Bligh had the real control of affairs. Macquarie reported later, Paterson was ‘such an easy, good-natured, thoughtless man, that he latterly granted Lands to almost every person who asked them, without regard to their Merits or pretensions’. Foveaux to Castlereagh, 20 February 1809, HRA, Series I, Vol. 7, p. 3.
 On 29 March 1809, Macarthur, Johnston and others sailed for England to participate in Johnston’s court-martial for mutiny arriving on 9 October.
 Like Foveaux, Paterson refused to intervene in the Bligh affair, Paterson to Bligh, 21 January 1809, HRNSW, Vol. 7, pp. 8-9.
 Paterson to Castlereagh, 12 March 1809, HRA, Series I, Vol. 7, p. 18.
 Agreement between Bligh and Paterson, 4 February 1809, HRNSW, Vol. 7, pp. 17-18, HRA, Series I, Vol. 7, pp. 45-46.
 Bligh’s Proclamation of his authority at the Derwent, 29 April 1809, HRNSW, Vol. 7, pp. 108-110, HRA, Series I, Vol. 7, pp. 96-99.
 Collins to Bligh, 4 May 1809, HRNSW, Vol. 7, p. 125 with Bligh’s response, 7 May 1809, HRNSW, Vol. 7, pp. 125-126.
 See Paterson’s Proclamation against Bligh, 19 March 1809, HRNSW, Vol. 7, p. 81.
 Duke of York to Castlereagh, 30 October 1808, HRNSW, Vol. 6, pp. 782-783.
 Nightingall to Castlereagh, 6 December 1808, HRNSW, Vol. 6, pp. 810-811; he accepted the commission. Nightingall to Castlereagh (?), 20 March 1809, HRNSW, Vol. 7, p. 64 on the onset of the illness that prevented him from taking up his commission.
 Macquarie’s Commission, 8 May 1809, HRNSW, Vol. 7, pp. 126-133 and his Instructions, 9, 14 May 1809, HRNSW, Vol. 7, pp. 122-140, 143-147.
 Proclamation, 4 January 1810, HRNSW, Vol. 7, pp. 255-257.
 Bligh to Castlereagh, 9 March 1810, HRNSW, Vol. 7, pp. 309-312.
 Macquarie to Castlereagh, 10 May 1810, HRNSW, Vol. 7, p. 378.
 HRA, Series I, Vol. 7, p. 331.
 Ibid, Ritchie, John, A Charge of Mutiny: The Court Martial of Lieutenant Colonel George Johnston for Deposing Governor William Bligh in the Rebellion of 26 January 1808 is the most detailed account. On 12 November 1811, Bligh published his account of the court martial.
 Cit, Yarwood, A.T., ‘Johnston, George (1764-1823)’, ADB, Vol. 2, p. 21.
 Cit, Yarwood, A.T., ‘Johnston, George (1764-1823)’, ADB, Vol. 2, p. 22.
 Foveaux to Earl Liverpool, 6 July 1811, HRNSW, Vol. 7, pp. 553-554 wishes to succeed Collins in VDL but in Liverpool’s response, 11 July 1811, HRNSW, Vol. 7, p. 555 his application was refused. On 18 July, Foveaux then asked Liverpool that arrears in pay owing him should be paid, HRNSW, Vol. 7, pp. 556-557.
 Martin Mason to Earl Liverpool, 26 January 1811, HRNSW, Vol. 7, pp. 490-491 recounted charges against Foveaux,
 Ibid, Whitaker, Anne-Maree, Joseph Foveaux: Power and Patronage in Early New South Wales, pp. 162-194 considers his career after 1812.