Brian Ahearn, descendant of convict Murtagh Ahern is author of ‘Beyond the Sea’ the life and times of Murtagh Ahern and the log of the convict ship ‘Atlas’ . In two volumes the 1,300 pages give a sweep of Irish history from Murtagh’s ancestor Brian Boru, the High King of Ireland, the dark days of Oliver Cromwell, the horrors and privations of the 1798 Irish rebellion to the discovery and founding of Australia. It details the history of the colony, the struggles of each succeeding Governor, the events and the characters who made Australia what it is today. The second volume includes the early Irish family records of Murtagh and Mary's family in Mileham.
The Atlas was built at Shields in 1801 and was in the service of the East India Company. Prisoners from throughout Ireland were embarked on the Atlas. They came from Limerick, Waterford, Wexford, Kilkenny, Kings Co., Queen's Co., Dublin, Carlow, Meath, Tipperary, Louth, Cork, Wicklow, Kerry, Kildare, Galway, Armagh, Roscommon, Mayo, Londonderry, Monaghan and Clare and were embarked at Dublin and Cork.
An Extract of a letter from Cork in the Freeman's Journal 29th October 1801 reveals that there was already illness on board when the vessel arrived in Cork from Dublin....
"A very severe sickness has prevailed on board the convict transports, who have arrived here from Dublin, particularly I understand in the Atlas. Great attention has been paid to their wretched condition by those whose duty it is to inspect their situations. Two of the convicts name Fagan and Conolly, have died. An attempt was made by some who were in the county gaol to effect an escape, but the plot was discovered by the attention and vigilance of one of the Wexford militia. The instrument they had used to break out, was a little bit of iron; with this they had picked out some stones in the centre kitchen, and to conceal their efforts in making the breach, they made use of an expedient which, it is understood, has been often employed by criminals on such occasions, viz, the burning of straw, wet for the purpose which made a smoke, almost sufficient to blind or suffocate. The gaoler, from the insecurity of the prison, is kept in great trepidation by those offenders, for fear any of them should escape."
Charles Bateson in The Convict Ships wrote of the voyage of the Atlas - "The Irish authorities permitted the prisoners to be embarked in a deplorable state of health, and the avariciousness, neglect and inhumanity of the master of the Atlas, Richard Brooks turned the voyage into one of the worst in the history of transportation. The Atlas embarked her first prisoners at Dublin. They were brought out to her in the three brigs and all were more or less unhealthy, suffering from Typhus or dysentery and should never have been embarked. The Atlas completed her complement of convicts at Cork where a number were convalescents from recent illness. Surgeon Elphinstone Walker viewed the embarkation of these prisoner with alarm but did not feel empowered to refuse to accept them."
Soldiers of the New South Wales Corps formed the Military Guard.
The Atlas departed Ireland for New South Wales on 28 November 1801, with 151 male and 28 female convicts and sailed via Rio de Janeiro and the Cape.
Elphinstone Walker later wrote to the Commissioner for Transport.......
Surgeon Walker to the Commissioners for Transport
Port Jackson 8th July 1802,
I have the honour to inform you of the arrival of the ship Atlas, Captain Richard Brooks, in this port on the 7th July 1801, and from the great mortality which has been on board I think it my duty to inform you of the cause. The first prisoners we embarked were from the three brigs that came from Dublin, one of which, named the Henrietta, were very sickly, and I was informed of the dysentery accompanied with a typhus fever. The other two brigs were also in a bad state of health. Most of the prisoners from the Henrietta were embarked on board this ship; we also embarked prisoners from the other two brigs.
The weather being then very cold, the washing of them and shaving their heads must, in my opinion, be very much against people in their sickly state. Some of them were embarked actually in the disease, and a great many convalescents. The rest of our prisoners embarked from Cork, many of whom were also convalescents. One old man, in particular, who was sent to be embarked was labouring under a very heavy sickness. Seeing that he could not survive long I thought it best to send him back, and he died before the boat reached Cork. One of the prisoners from the Henrietta died five days after he came on board; another also died before we left the harbour, which was on 28th November 1801.
After sailing from the Cove of Cork we experienced very bad weather, and the convalescents began gradually to relapse into their former sickness. When we arrived at Rio de Janeiro 30th January 1802, I had upwards of seventy sick, and was then myself recovering from a very heavy sickness. The prisoners were put on shore on one of the small islands for the recovery of health, and the number of sick began now to diminish from the benefit of fresh provisions and other comforts. We lost by sickness fifteen male prisoners and a soldier from the time of their embarking till our arrival, and during our stay two male prisoners and one female died.
RIO DE JANEIRO
We sailed from Rio de Janeiro 26th February 1802.
A short time after leaving that port a general sickness prevailed amongst the soldiers, which I attributed to poison, and I at the same time had a return of my sickness.
A mutiny was at this time going on amongst the prisoners, which on being discovered caused them to be more closely confined, and which consequently was much against the sick.
CAPE OF GOOD HOPE
We arrived at the Cape of Good Hope 12th April 1802, having lost by sickness six male prisoners, one soldier and serjeant's wife on our passage between Rio de Janeiro and the Cape. The number of the sick was now considerably diminished. We had here a supply of fresh provisions for the prisoners. I also obtained a supply of some medicines and fumigating apparatus. During our stay here we lost one male prisoner. We sailed from the Cape on the 19th April, some time after leaving which port the scurvy made its appearance, which soon became general, and amongst those who were formerly sick it made great havock. Having few or no antiscorbutics, I was forced to palliate with medicines.
The weather was in general very bad from the time of our leaving the Cape till on arrival at Port Jackson, and we lost by the scurvy and dysentery forty three male prisoners and one female, several of whom were after our arrival, at which time I kept about twenty of the worst of my patients on board, they being incapable of being removed, and had a supply of necessaries for them from the hospital. They soon began to recover from the benefit of the vegetable diet. By this gentlemen, I have endeavoured to state, from as exact a point of view as I possibly could, the causes of the great mortality which has prevailed on board this ship. 
SURGEON THOMAS JAMISON
The situation of the Passengers was unpleasant in the extreme. Surgeon Thomas Jamison's cabin was filled with provisions and Richard Brooks stowed packages in there as well so that he was constantly being disturbed. Thomas Jamison left the Atlas at Rio De Janeiro and embarked on the Hercules for the remainder of the voyage to Port Jackson.
Surgeon Jamison (acting principal surgeon) to Lord Hobart,
His Majesty's Service being materially concerned in the Subject which I am now about to submit to your consideration, I cannot doubt that you will deem my inducement hereto some apology for the liberty I take in trespassing on your patience.
Were I tacitly to pass over the complicated abuses committed on board the Atlas Transport, I should consider myself highly reprehensible. A due sense of moral duty urges the information contained in this letter, and I shall neither exaggerate or diminish the facts it states, but detail the circumstances I communicate truly as they occurred in the hope that if attended to I may be the instrument of future benefit to His Majesty's Service, in preventing a repetition of abuses disgraceful to humanity, by bringing the offender in the present Instance to such just punishment as the nature and extent of his offences may seem to deserve.
The principal matter of complaint I have to enter into against Mr. Richard Brooks Master of the Atlas (and whence originates various causes of accusation), is that he shipped on board said vessel under his command a far greater quantity of goods and merchandize for his own private trade than could be possible warranted by the usage of the Service he was engaged in. By such conduct the ship was so deeply laden that it became necessary to keep the air scuttles in general closed, and the deadlights frequently shut in.......The usual modes of preserving health and cleanliness on shipboard was seldom attended to, even the Hammocks and bedding were as permanent fixtures and salutary custom of airing them upon deck being generally omitted. From the above circumstances and the humidity created by the confined state of the convicts the air became noxious to such a degree as to extinguish the candles burning the cabin.....
ILLNESS ON BOARD
The just observation that foul air and filth generate disease was verified in the Atlas. A dangerous fever and dysentery appeared amongst the convicts, to which numbers fell victims; nor were the necessary means adopted to check the progress of this destroying Malady used; on the contrary it should see, from the conduct pursued, that it was intended to aid the baneful influence of this harbinger of Death, for one half the hospital was occupied as a sail room, and by this arrangement the Sick were some of them obliged to sleep in the prison with other prisoners who were in health. The prevailing disease being contagious in its kind, the infection extended from the cause above recited, and the malady became almost general I have further to remark upon the above head that when the ship lay at Rio, the prisoners being kept on shore presented a favourable opportunity to expel infection from on board by washing and fumigation; but the Surgeon could do neither to effect, the prison being almost filled with sundry kinds of lumber, principally Mr. Brooks private property...........
On the upper deck the Spars were raised three or four feet high on each side in the waist, and the long Boat placed in the centre; the main hatchway was stowed full of casks, that not a breath of air could pass down into the prisons, and the stantions of the after Hatchway was boarded up so close that it was impossible that a breath of air could pass that way; the wind sails were without hoops to expand the canvas of which they were formed; and being also never repaired, or otherwise attended to , that it was only the name, being every way uncalculated to answer the purposes of utility for which they were intended.
The afflictions of the ill fated beings did not cease here. The water daily issued and called three pints did not exceed a beer quart (infinitely too little for men on a constant salt regiment) and that the thirst and hunger they endured might bear some proportion to each other, they were defrauded of a great part of their ration of provisions; all the sick were confined to what they termed a vegetable diet, which consisted of pease, barley rice, and oatmeal; their animal food entirely withheld, altho' the full ration is charged to Government; their being deprived of their beef and pork and curtailed in the species given as an equivalent in lieu by false weights and measures, together with the filth wretchedness of an insupportable durance, soon induced that debility which eventually terminated in a typhus fever and scurvy; and as it should seem that avarice and cruelty were the predominant features in the character of Mr. Brooks he carried the further exercise of cruelties on these pitiable objects to a degree that almost exceeds the bounds of credibility. It was no uncommon spectacle to behold these suffering people labouring under the extraordinary encumbrance of two pair of heavy irons on their legs and one round the neck with a large padlock as an appendage that weighed at least a pound and a half. The poor creature, almost strangled and sinking under his burden of afflictions must perforce remain thus situated night and day, till a capricious change in the disposition of his tormentor should lead him to remit the punishment.
Amongst other incentives to Sickness, as also a preventative to a recovery of the afflicted, was a rule adopted on board the Atlas to extinguish the fires (used for dressing the Provisions) at the hour of dinner, which rendered it impossible for the Surgeon to cause drinks or other comfortable ailments to be prepared for his patients. 
Later Thomas Jamison took legal action against Richard Brooks and made the following Affidavit:
I came rather late in the Evening on board the Ship Atlas on Saturday the Twentieth day of February in the Year One Thousand eight hundred and two, said Vessel then lying in the Harbour of Rio Janeiro, on descending the After Ladder, I found the Steerage so blocked up that the way to my cabin was utterly impeded by packages stowed there; I endeavoured with my foot to remove them, but not succeeding in my efforts to obtain a passage; by pushing out of my way a case which effectually prevented my progress, I laid hold of it with my hand, when the part I held broke off, and with much difficulty, I at length reached my Cabin. Shortly afterwards (having undressed) I put on my dressing gown and went on deck. Mr. Byron first Mate of the Atlas addressed himself to me, Ironically saying he was much obliged to me for breaking open his case, (meaning the Case I had removed) and exposing his property to the sailors in the steerage; I told him in reply that he was not obliged to me, and that there was no personality intended by me in removing the case in question, as it prevent my going into my cabin; Mr. Bryon in a style of much haughtiness demanded to know, if I wanted to Command the ship; I replied that I neither wanted to command or to interfere in anything relating to the ship; but as the Atlas was in His Majesty's Service and myself a Kings Officer and ordered a cabin in her for my accommodation I of consequence expected a passage to it;...Richard Brooks master of the Atlas being then in his bed called out from the cabin where he lay and asked what noise that was on deck. Mr. Byron replied that some words had taken place between him and Mr. Jamison. Mr. Brooks then said Mr. Byron put that mutinous scoundrel (meaning me) in irons; irritated by such illiberal language I told Mr. Brooks he lied, and that I was neither mutinous nor a scoundrel without further altercation Mr. Brooks came out of his cabin, struck me repeatedly and to prevent all possibility on my part of resistance or defence, I was forcibly held by Mr. Byron, Mr. John Willen and others; I was knocked down on the deck by Mr. Brooks and being down, then overpowered by him and his adherents in such defenceless situation with unmanly violence he mad repeated blows at me until he had vented his savage and brutal passion when he returned again to his cabin. 
The Atlas arrived in Port Jackson on 6 July 1802.
Elphinstone Walker compiled a return relating to the convicts on arrival:
151 male convicts and 28 female convicts were received on board at Cork
Died on the passage: 2 soldiers and 1 serjeant's wife; 63 male convicts and 2 female convicts;
three male convicts escaped.
85 male and 26 female convicts arrived in the colony.
DEPARTURE FROM PORT JACKSON
The Atlas departed Port Jackson bound for China on 7 October 1802.
5). In 1810 the following people who had arrived on the Atlas received their Certificates of Freedom being restored to all the Rights of Free Subjects in consequence of their terms of transportation being expired... Lawrence Farrell, Thomas Kennedy, Elizabeth McNamara, Richard Collier, Martin Sweeney, John Graham, Mary Redmond, Mark Flood, Elizabeth Cook, John Morgan tried in Meath.
6). National Archives - Voyages: (1) 1801/2 New South Wales and China. Capt Richard Brooks. Deptford 16 Jul 1801 - 20 Aug Blackwall - 19 Sep Waterford - 23 Sep Cork - 2 Feb 1802 Rio de Janeiro - 12 Apr Cape - 7 Jul Sydney Cove - 14 Dec Whampoa - 18 Apr 1803 St Helena - 18 Jun Deptford
7). The Atlas returned to Australia with convicts in 1819
Michael BolandKings Co. 1800
James Cook tried in Meath 1801
Cornelius Dwyer tried in Limerick 1802
William Gorman tried in Waterford 1801
Sir Henry Brown Hayes tried in Cork City 1801
John Morgan tried in Meath 1801;
Mary Redmond/ McDonough tried in Waterford 1801