Some 6000 years ago, Austronesian peoples (descendants of the early Chinese) migrated into Indonesia, the Philippines, and New Guinea, where they encountered other societies that had been there for many thousands of years. How, according to Guns, Germs, and Steel, can we explain the different outcomes of these encounters in Indonesia and New Guinea?
The answer to this question can be found in Chapter 17 of the book. Specifically, it can be found beginning on p. 350 of the paperback edition. When thinking about the answer, we should remember the main theme of the book. The main theme of the book is that geography leads to agriculture and agriculture leads to powerful societies. Thus, we should expect that different outcomes would be due to differences in geography and agriculture.
This is, indeed, what Diamond argues at this point in the book. On p. 351, he says that Indonesia was dominated by Austronesians and New Guinea was not. He says that this is because
The residents of Indonesia were still hunter-gatherers, while the residents of New Guinea were already food producers…
Because the people of New Guinea lived in a place that was good for farming, they were able to be strong enough to resist the Austronesians. They had dense populations, supported by farming, that were able to fight off the intruders. By contrast, Indonesia was less suitable for agriculture and therefore only had a small population of hunter-gatherers who were not strong enough to resist.
Thus, the different outcomes in New Guinea and Indonesia are due to the fact that the former had agriculture while the latter did not.