The Scarborough then departed Portsmouth 19th January 1790 as part of the Second Fleet.
There were plans of mutiny on the voyage of the Scarborough however they came to nothing when one of the prisoners informed the Captain....The Annual Register recorded the following account of Samuel Burt....
A letter has been received fromSamuel Burt, the person convicted of forgery, but pardoned on condition of going to New South Wales; dated from on board the Scarborough transport, False Bay, which contains the following account: On the 12th February, our ship having separated from the Surprize transport, the Neptune being a great way ahead, and the sea perfectly calm, the convicts began to whisper from one to the other their mutinous intentions; the plot being communicated to myself, I readily agreed to the scheme, assenting to every proposal of plunder and murder, until such time as I became completely master of the conspiracy, and the ringleaders of it. I then apprised the captain of the ship, and the military officers, of the danger they were likely to encounter; and so thoroughly did my information prepare them for the business, that with little or no trouble the ringleaders were secured, and the scheme entirely frustrated. The particulars being enquired into, they made such confessions that human nature would almost shudder at the thoughts of. Several of them have been flogged with the greatest severity, and others of more dangerous description are at this time chained to the deck and it is supposed will be tried and executed immediately on their arrival in New South Wales'. The circumstances of Burt's case were rather remarkable. Being rejected by a woman whom he wished to marry, he committed a forgery, and immediately afterwards surrendered himself at Bow street, for the purpose of getting hanged. Being considered as an object of compassion, he was offered his majesty's most gracious pardon, which he twice or thrice refused. The lady at length consented to marry him, and he then became as solicitous to live, as he had before been anxious for death; but, during her repeated visits to him in Newgate, she caught the gaol fever, and died. - Annual Register.
The Guardian store ship on the passage to New South Wales had been wrecked in December 1789, however under the direction of Captain Riou had managed to make it to False Bay at the Cape. Lieut. Riou wrote to Secretary Stephens in May 1790 informing him of some of the details of the wreck and of the articles he had put on board the vessels of the Third Fleet to be taken to New South Wales
The Neptune, Surprise and Scarborough arrived in False Bay the 14th April, and in them I sent, under the care of Lt. John Shapcote, the agent, twenty convicts which were all that remained alive of the twenty five that were sent on board the Guardian at Spithead. I also put on board those ships four hundred tierces of beef and two hundred tierces of pork; and had not a misunderstanding existed between Lieutenant Shapcote and myself, it is my opinion I could have sent many articles which would not have taken up much stowage in the ships under his direction that would have been very acceptable to his Majesty's colony in new South Wales. But as that officer waited my orders for his proceedings and afterwards persisted in his own resolution of sailing from False Bay on a certain day which he determinately fixed upon, I lost no time to endeavour to acquiesce in his measures, resolving that nothing should be wanting on my part to give all possible assistance to the colony, fearing that it might severely experience the effects of the accident that has befell his Majesty's ship under my command. The Neptune, Surprize and Scarborough sailed from False Bay on the 29th April. 
Twelve of the surviving convicts of the Guardian were embarked at the Cape on the Neptune and eight on the Scarborough. 
The remainder of the Second Fleet - the Surprize, Neptune and Scarborough arrived in Port Jackson on 28 June 1790
The military guard was a detachment of New South Wales Corps sent to replace the Marines.
The mortality rate on the Scarborough as with the Surprize and Neptune voyages of 1790 was horrific. - The rations of the prisoners in the Scarborough were not deliberately withheld but owing to the reported mutiny, convicts were very closely confined. It was to this fact that the high death rate was directly due. - .
Judge Advocate David Collins described the scene on the landing of the prisoners: - On the evening of the 28th the Neptune and Scarborough transports anchored off Garden Island, and were warped into the Cove on the following morning. By noon the following day, two hundred sick had been landed from the different transports. The West side afforded a scene truly distressing and miserable; upwards of thirty tens were pitched in front of the hospital; all of which as well as the adjacent huts, were filled with people, many of whom were labouring under the complicated diseases of scurvy and dysentery, and others in the last stage of either of those terrible disorders, or yielding to the attacks of an infectious fever. The appearance of those who did not require medical assistance was lean and emaciated. Several of these miserable people died in the boats as they were rowing on shore, or on the wharf as they were lifted out of the boats; both the living and the dead exhibited more horrid spectacles than had ever been witnessed in that country.
Rev. Richard Johnson described his visit to the Surprize: - a great number of them laying, some half and others nearly quite naked without either bed or bedding unable to turn or help themselves. Spoke to them as I passed along, but the smell was so offensive that I could scarcely bear it. Johnson was persuaded not to venture into the Scarborough's prison.
The Scarborough departed Port Jackson bound for China in August 1790.
Escape from the Colony
In September 1790 several prisoners who had arrived on the Scarborough made their escape from the colony in a boat. They were thought to have perished, however were found five years later in the Port Stephens district having lived with a native tribe for the intervening years. Their names were John Tarwood, a daring, desperate character, and the principal in the scheme; George Lee; and George Connoway.
Notes and Links
1). Sixty eight prisoners of the Scarborough were reported to have died on the voyage.
2). Emancipist and Merchant James Larra arrived as a convict on the Scarborough
3). Surgeon Daniel Kelly arrived as a convict on the Scarborough