Nearly every major stone age culture outside of Europe fell to European colonialism, they were immunized against the diseases they brought with them as well as their advanced technology made it nigh impossible to defend against them. Even the great empires of the Inca and the Aztecs fell.
The biggest weapon of the Europeans was the hidden one, disease. The great plagues of history ravished the New World as well as all other foes. Even one plague can bring empires to their knees, never mind multiple simultaneous plagues, never mind small population sizes.
Somewhere in the age of colonial Europe, Atlantis was discovered in the Pacific (I know right, wild!). It is fairly large and full of pesky native empires. Of course they must be dealt with, so Europe is prepared to Aztec them and destroy their empires, but this one empire (let's call it Aborigia) refuses to sit down and take it.
How can a stone age empire (akin in this case to the Aztecs) possibly defend itself against the various Colonial powers of Europe in 1500?