Over the next two years, Bligh made enemies not only of Sydney's military elite, but several prominent civilians, notably John Macarthur, who joined Major George Johnston in organising an armed takeover.

He was kept in confinement in Sydney, then aboard a ship off Hobart, Van Diemen's Land, for the next two years while Johnston acted as Lieutenant-Governor of New South Wales.

It is likely that he was deliberately selected by the British government because of his reputation as a "hard man" and was expected to have a good chance of reining in the maverick New South Wales Corps; something that his predecessors had not been able to do.

[6] The president of the court, Sir Isaac Coffin, wrote to the Admiralty and made several serious accusations against Bligh, including that he had influenced the officers to testify against Short.

[7] Soon after his arrival at Sydney, in August 1806, Bligh was given an address of welcome signed by Major George Johnston for the military, by Richard Atkins for the civilian officers, and by John Macarthur for the free settlers.

However, not long after, Bligh also received addresses from the free and freed settlers of Sydney and the Hawkesbury River region, with a total of 369 signatures, many made only with a cross, complaining that Macarthur did not represent them.

On 31 December 1807 Robert Stewart, Viscount Castlereagh, Secretary of State for War and the Colonies, wrote back to Bligh with instructions to stop the barter of spirits.

[8] He argues that the enmity of the monopolists within the colony stemmed from this prohibition and other policies which counteracted the power of the rich and promoted the welfare of the poor settlers.

[6] He dismissed D'Arcy Wentworth from his position of Assistant Surgeon to the Colony without explanation, and sentenced three merchants to a month's imprisonment and a fine for writing a letter that he considered offensive.

Jamison was the highly capable (if crafty) Surgeon-General of New South Wales, and had accumulated significant personal wealth as a maritime trader; he was also a friend and business partner of the powerful Macarthur.

In October 1807 Major Johnston wrote a formal letter of complaint to the Commander-in-Chief of the British Army, stating that Bligh was abusive and interfering with the troops of the New South Wales Corps.

Bligh stopped Macarthur from cheaply distributing large quantities of rum into the Corps and halted his allegedly illegal importation of stills.

When Parramatta returned to Sydney in December 1807, the bond held to ensure that masters and owners of vessels did not help prisoners escape the colony was deemed to be forfeited.

Johnston replied that he was ill,[6] as he had wrecked his gig on the evening of 24 January on his way home to his farm after dining with officers of the Corps.

This petition was signed by the officers of the Corps and other prominent citizens but, according to Evatt, most signatures had probably been added only after Bligh was safely under house arrest.

[6] They were hindered by his daughter and her parasol,[9] but Captain Thomas Laycock finally found Bligh, in full dress uniform, behind his bed where he claimed he was hiding papers.

[13] Johnston took control with the rank of lieutenant-colonel on 25 April 1808[citation needed] and appointed Charles Grimes, the Surveyor-General, as Judge Advocate.

[14] Another prominent opponent of Bligh, Macarthur's ally Thomas Jamison, was appointed as the colony's Naval Officer (the equivalent of Collector of Customs and Excise) and also reinstated as a magistrate.

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.

[18] Following Bligh's overthrow, Johnston had notified his superior officer, Colonel William Paterson, who was in Van Diemen's Land (now called Tasmania) establishing a settlement at Port Dalrymple (now Launceston), of events.

However, Bligh sailed to Hobart in Van Diemen's Land, seeking the support of Lieutenant-Governor David Collins to retake control of the New South Wales Colony.

Collins refused to support him[13] and on Paterson's orders, Bligh remained cut off on board Porpoise, moored at the mouth of the River Derwent south of Hobart, until January 1810.

[22] Macquarie reinstated all the officials who had been sacked by Johnston and Macarthur, replaced the alcoholic Atkins with Ellis Bent (the first professional lawyer to occupy a public post in Australia) as Judge Advocate,[23] and cancelled all land and stock grants that had been made since Bligh's deposition.

[6] Macquarie had been impressed with Foveaux's administration, putting his name forward to succeed Collins as Lieutenant-Governor of Tasmania because he could think of no one more fitting; and considered that he could not have acted otherwise with regard to Bligh.