[6] Under Brooks's command, between 1801 and 1803 Atlas sailed for the East India Company on a voyage that first had her carrying convicts from Ireland to Port Jackson, and then going on to China, before returning to England.

Governor Philip Gidley King censured Brooks for this high death rate, which was the result of his negligence and the overcrowding that his transport of his personal cargo caused.

[8] Following the resumption of war with France in early 1803, concern developed in Britain about Napoleon's planned invasion of the United Kingdom.

The British East India Company in November voted to underwrite 10,000 tons (bm) of armed transports to protect Great Britain's coasts.

In the fall of 1805 a small naval squadron under the orders of Commodore Sir Home Popham escorted a fleet of transports, including Atlas, and East Indiamen carrying some 5000 soldiers under the command of Major-general Sir David Baird to attack the Dutch at the Cape of Good Hope.

The expedition sailed again on the 26 November, and on 4 January 1806, in the evening, anchored to the west of Robben Island, preparatory to taking the Dutch colony.

[a] Lloyd's Register for 1806 still showed Atlas with G. Pilmore, master, and Temple & Co., owner, with her trade as London–Botany Bay.

[16] As late as 1808, Lloyd's Register still showed Pilmore as master of Atlas and her trade as Botany Bay.

British ships were then free to sail under a license from the EIC to India, the Indian Ocean, or the East Indies.

[19] In February 1818 Atlas, Joseph Short, master, was sailing from Dundee when she encountered a Portuguese brig with 360 slaves from Mozambique.