Possible spoiler alert: I have tried to avoid giving away any pertinent plot points, but if you haven't read the book, perhaps you should look away now, and come back afterwards. I've found that having an idea of the general geography is very useful - not only on the first run-though of the canon, but on the second, third, fourth ...
The Nutmeg of Consolation departed Batavia  (the site of current-day Jakarta) and had trouble weathering the nearby Cape Krawang (or Karawang).She then sailed through the Strait of Makasar into the Celebes Sea, where she met the Dutch merchantman Alkmaar .
She proceeded to the Island of Nil Desperandum  at the mouth of the Salibabu (or Salebabu) Passage, where the Cornelie was watering.
Cornelie pursued Nutmeg through the Passage, to the inevitable battle .
At this stage, it is impossible to chart the rest of the journey with any accuracy. Jack Aubrey takes the ship to Sweeting's Island, a remote island discovered by Carteret (a cousin on Jack's mother's side). My best guess at its location is based on a map of Carteret's voyage, which indicates two islands around the location of what are now known as the Sonsorol Islands . After leaving Sweeting's, the ship headed generally eastward in search of the south-east trades.
We know where they sailed from (north of New Guinea) and we know where they went (to Port Jackson and Sydney Cove). We also know where they didn't go - anywhere near the Great Barrier Reef. But O'Brian gives few indications of the actual route.He does say that they met a canoe full of Solomon Islanders and bought some pigs from them, and he hints that they do not go very near Norfolk Island. But the only landfall is the Angerich shoal, of which I have found no mention in maps or gazetteers. O'Brian might have based the location of this shoal on Middleton Reef or Elizabeth Reef, which I've marked with a blue star.
Dean King's Harbors and High Seas suggests that the route may have taken them out between Vanuatu and Fiji and then south-west between New Caledonia and Norfolk Island. Perhaps this is what O'Brian had in mind.
Sydney Cove was the first point of European settlement in Australia in 1788. By the time of Jack and Stephen's arrival, the town had spread a little way out from the shores of the Cove - mostly southward, but also to the west where Parramatta was established.
The first Government House  was built near the wharf . The site is now the location of the Museum of Sydney, and the "new" Government House is on the bluff  above Bennelong Point. Dr Redfern's Hospital  was on the western side of the Cove, in the location now known as The Rocks. To the north, the Sydney Harbour Bridge  now spans the half-mile gap to the North Shore, while to the east the Sydney Opera House  sets sail into the waters of Port Jackson. Dr Maturin would be delighted to spend many hours in what is now the Botanic Gardens .
While the ship was lying at its various berths in Sydney Cove , Maturin and Martin made two journeys. The first was to the west and south-west, passing Parramatta  on the way to Gregory Blaxland's property  at the foot of the Blue Mountains. They then headed south for a while and then east, to return to Sydney Cove via Botany Bay.
The second journey is harder to chart. We're told that they made a trip of three days to Woolloo-Woolloo, which is inland from Bird Island - not an impossible trip, but one that would tax two townsmen not familiar with the bush. The bigger problem with the journey, though, is the water that they'd have to cross. Broken Bay and the Hawkesbury River flowing into it would be impassible for many miles upstream, but there's no mention of this in the book. Indeed, there are several references to staying close to the shore during the journey. So, we'll just have to grant O'Brian a touch of magic realism about this one.
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