The failed insurrection of August and the removal of the suspected Irish leaders to remote parts of the colony did not dampen the convicts’ enthusiasm for organised rebellion. In September of 1800 another insurrection was planned. This one was to use the pikes that had not already been found. The rebels were to assemble at Parramatta on a Sunday morning when the local authorities and hierarchies would be in Church service. There the rebels would overpower the soldiers and then march on Sydney. The leaders used an escaped convict, John Lewis to send messages from farm to farm. Unfortunately Lewis was captured, gaoled and eventually talked of the rebellion. From the information Lewis gave, Captain John MacArthur of the NSW Corps received a shakily written letter that relayed that a ‘Croppie’ uprising was about to occur. MacArthur’s advice to the Governor was to wait for the convicts to rebel and once they were out in the open deal with them. The rebel leaders learned that their plan had been discovered and halted their operations. Marsden once again zealously set about trying to discover the hidden pikes. Several more informants came forward and one named the still gaoled Bryan Furey as a pike maker. From the increasing information the NSW Corps was able to round up the ringleaders; William Silk, Micheal Quintan, Maurice Wood, John Burke and Thomas Brannon. They were flogged and isolated from the general convict population on the hulk Supply in Sydney Harbour. The remainder of the rebels were given either five hundred or two hundred lashes.
The authorities seem to have feared that Holt, an experienced rebel leader, would be a centre of disaffection, but nothing was farther from his plans. As a lower middle-class Irish Protestant with firm notions of respectability Holt wanted to better his position by thrift and hard work and remained divorced from what he saw as impractical insurrection. Despite this, he was implicated as a leader in the rebellion but without substantial proof of his involvement he was spared the lash as was Harold.  As a form of punishment for their suspected complicity with the rebels both Holt and Harold, who were still being detained from the previous insurrection, were made to watch the floggings of two convicted offenders, Maurice Fitzgerald and Paddy Galvin on the orders of Judge-Advocate Richard Atkins and Marsden. Holt left a vivid account.
The place they flogged them their arms pulled around a large tree and their breasts squeezed against the trunk so the men had no power to cringe ... There was two floggers, Richard Rice and John Johnson the Hangman from Sydney. Rice was left-handed man and Johnson was right-handed, so they stood at each side, and I never saw two threchers in a barn move their strokes more handier than those two man-killers did....
No aspects of Marsden’s activities did more harm to his pastoral work or to his historical character in Australia than his reputation for extreme severity as a magistrate. This particular action was scarcely defensible, but Marsden was not the only magistrate who ordered the infliction of illegal punishments.
In 1801, the transport ship Anne arrived at Sydney with 69 United Irishmen out of the 178 convicts on-board. Governor King was disturbed as the rebel leaders from the previous rebellions had been uncovered and sent to remote parts of the colony. The arrival of the Anne promised another group of United Irishmen leaders who could cause problems in the convict population, a view reinforced by the convict mutiny on the ship en route. The Anne brought news of Irish Union and King hoped that this would persuade the Irish convicts to accept their fate in Australia. This proved a forlorn hope. The Irish political prisoners had been fighting against English rule for several years and wanted to go home. The main opponent in their way to getting home was the British authorities in Sydney and Parramatta. During the next year four more rebellion plots were uncovered. All were foiled by informants in the convict population. Two of the plots involved escaping by ship, either by seizing a ship or seeking passage on a French ship. The Governor was so concerned that convicts would escape by sea such that even in 1804 with word of a possible convict uprising. Several American ships were sent out of Sydney Harbour on King’s orders because he suspected that they would be sympathetic to the rebelling Irish convicts. 
In 1803 there were still outstanding issues for the Irish convicts. The idents stating the term the prisoners were to remain exiled in NSW still had not arrived from England. Until the idents arrived all Irish prisoners were stuck in the penal colony. There continued to be escape attempts by convicts both English and Irish. Inevitably the escapees would raid nearby farms for liquor and firearms. In February 1803, fifteen convicts escaped from a farm at Castle Hill and raided the farm of Verincourt de Flambe for liquor, silverware and firearms. Two of the convicts, Patrick Gannan and Francis Simpson went on to the farmhouse of James Bean and raped his seventeen year old daughter but were captured two days later asleep in the bush and hanged.