Those who had taken power were not confined by the effective operation of the rule of law, save insofar as ultimate retribution from London was anticipated. Until a superior officer to Johnston arrived six months after the coup, John Macarthur was effectively in control. During that period the rudimentary legal system was abused, where not suspended and the courts used as a tool of political revenge. Magistrates loyal to Bligh were dismissed. Other loyalists were subject to a parody of justice. Gore and George Crossley, the dubious ex-lawyer who had some role in advising Bligh on the rebellion were convicted on bogus charges and transported to the coal mines at Newcastle for seven years. In March 1809, John Palmer, Bligh’s Commissary was charged with sedition for distributing Bligh’s Proclamation that the Corps was it a state of mutiny, denied the competency of the court and refused to plead but was unlawfully gaoled for three months and fined £50. The civil court processes were also abused. However, with the exception of these politically motivated cases, the legal system continued to operate more or less as before. Commerce was adversely affected as it was uncertain whether the negotiable bills payable in sterling that had traditionally been used for transactions with the government, would be honoured in London. No one who lived through these months was in little doubt that the rule of law was severely compromised.
Atkins was replaced and Johnston initially appointed Charles Grimes, the Surveyor-General, as Judge-Advocate and ordered that Macarthur and the six officers be tried; on 2 February, they were found not guilty. By contrast, Bligh supporters were sentenced harshly with Provost-Marshall Gore sentenced to seven years for causing the arrest of Macarthur. On 3 April, Grimes resigned after George Johnston, who was acting as governor, had criticised some extraordinary proceedings in the court over which he presided. Though these were partly due to his ignorance of the law or, as Johnston said, ‘errors of judgment more than of design’, Grimes was regarded as one of the opponents of his administration. Macarthur was then appointed as the so-called ‘Secretary’ and effectively ran the business affairs of the colony. Another prominent opponent of Bligh, Macarthur’s ally Thomas Jamison, was made the colony’s Naval Officer (the equivalent of Collector of Customs and Excise). Jamison was also reinstated as a magistrate, which enabled he and his fellow legal officers to scrutinise Bligh’s personal papers for evidence of wrong-doing by the deposed governor. In June 1809, Jamison sailed to London to bolster his business interests and give evidence against Bligh in any legal prosecutions that might be brought against the mutineers. Jamison died in London at the beginning of 1811 and did not have an opportunity to testify at Johnston’s court martial later in the year. However, the unity of the rebels quickly dissipated.  Johnston and Macarthur fell out with Blaxland and Macarthur even managed to alienate the NSW Corps previously his staunchest supporters.
 Johnston did not inform Castlereagh of Bligh’s arrest until 11 April 1808, HRNSW, Vol. 6, pp. 575-589. For correspondence between Bligh and the rebels see, Johnston to Castlereagh, 11 April 1808, HRA, Series I, Vol. 6, pp. 242-271 and Johnston’s General Orders, HRA, Series I, Vol. 6, pp. 271-276.
 HRNSW, Vol. 6, pp. 435-453, Johnston to Castlereagh, 11 April 1808, HRA, Series I, Vol. 6, pp. 276-291 print the Colonial Secretary’s Papers of the examination of officers after Bligh’s arrest.
 Government and General Order, 27 January 1808, HRNSW, Vol. 6, p. 453.
 Allars, K.G., ‘Crossley, George (1749-1823)’, ADB, Vol. 1, pp. 262-263.
 Steven, Margaret, ‘Palmer, John (1760-1833)’, ADB, Vol. 2, pp. 309-311. See also, Palmer to Bligh, 2 March 1808, HRNSW, Vol. 6, pp. 530-531 in which he reaffirmed his support for Bligh.
 Palmer was reinstated by Governor Lachlan Macquarie but failed to receive any official compensation for deprivations suffered in the rebellion. Though the secretary of state instructed Macquarie to examine the commissariat accounts and see that the office was placed on a proper footing, he observed that as the complaints against Palmer ‘have been chiefly brought forward since the arrest of Governor Bligh, it is probable they are exaggerated’. Palmer’s examiners at the Comptroller’s Office in London held that the charges ‘seemed to have arisen as much from private pique as from zeal for the public service’ and were too vague to justify a formal inquiry. However, they thought it inexpedient to restore Palmer because of his long tenure in office (since 1791) and recommended the appointment of another commissary. On 25 July 1811, Palmer was demoted to assistant commissary and placed on half-pay and next year the entire commissariat system was reorganised.
 Ibid, Kercher, B., Debt, Seduction and Other Disasters: The Birth of Civil Law in Convict New South Wales, pp. 41-42.
 Curry, J.E.B., Reflections on the Colony of New South Wales: George Caley, (Lansdowne), 1966, p. 157.
 He was, however, reinstated as Judge-Advocate on 13 December 1808, a decision he accepted despite having played the critical role in the case that precipitated the rebellion. Aitken’s conversion to the rebel cause was motivated largely by financial considerations, the capacity of the Corps to pander to his alcoholic tastes and a free grant of 500 acres in the Minto District.
 Dowd, Bernard T., ‘Grimes, Charles (1772-1858)’, ADB, Vol. 1, pp. 487-488 and ‘Charles Grimes: The Second Surveyor-General of New South Wales’, Journal of the Royal Australian Historical Society, Vol. 22, (4), (1936), pp. 247-288.
 HRNSW, Vol. 6, pp. 465-510 and HRA, Series I, Vol. 6, pp. 291-352 detail the trial. Johnston then appointed Anthony Fenn Kemp to the post. Aitkens and especially Kemp and Grimes were incompetent but more importantly made judicial decisions unfavourable to Macarthur. Foveaux had little choice but to reinstate Aitkens: Foveaux to Castlereagh, 20 February 1809, HRA, Series I, Vol. 7, p. 2 ‘I had no choice left but to restore Mr. Atkins, or expose the public to the serious inconveniences which must inevitably have followed from leaving so indispensable a department vacated.’
 Gore denied the authority of the rebel court that would not give bail and refused to plead; he was kept in gaol without trial for more than two months, and in a letter to Bligh unfavourably compared his treatment by the NSW rebels with that by the Irish rebels ten years before. On 30 May Gore was again brought before a rebel court and again refused to plead. He was sentenced to transportation for seven years and was sent to Coal River (Newcastle) where he laboured with ordinary convicts. See, HRA, Series I, Vol. 6, pp. 555-563 for a statement of Gore’s refusal to recognise the court, his defence and correspondence with Bligh.
 Government and General Order, 12 February 1808, HRNSW, Vol. 6, p. 519.
 Macarthur to Captain Piper, 24 May 1808, HRNSW, Vol. 6, pp. 643-644 indicated that unity was short-lived: ‘...some of our old acquaintances have behaved most scurvily...’
 Johnston to Castlereagh, 30 April 1808, HRA, Series I, Vol. 6, pp. 453-516 provides details for the reasons behind the rift between the Blaxlands and Johnston and Macarthur.
 Johnston to Castlereagh, 30 April 1808, HRA, Series I, Vol. 6, pp. 518-520.