Now, this is a short myth, similar to Manu and the Fish, but it has the same kind of importance to it. The gods are out to destroy humanity because they have become barbaric, murderous, and no longer respect the gods. The gods are somewhat miffed at such behavior, so they want to hit the reset button by flooding the world. It’s understandable, and will hardly be the last time this idea comes forth. But the two brothers are examples that there is some good in humanity because they treated the llamas well, so the llamas warn them. The Incan flood is interesting because it is one of the few that doesn’t involve a boat.
Instead of a boat, the brothers and their families ascend the mountains after they receive the warning from the llamas. As the rains keep coming down, the waters get higher and higher, and to compensate, the Andes Mountains grow taller from the ground in order to keep them safe from the rains. After the flood has ended, the mountains recede, and the humans descend to rebuild. The llamas, however, stay up in the mountains in case the flood ever happens again.
Like with Manu, and this is a trend in all of them, the flood myth establishes a baseline of acceptable behavior. They are kind and humble, whereas the barbarous people have offended the gods, and will be destroyed. While "Manu and the Fish" was more ambiguous with the idea of karma, this myth establishes a clear moral code of what is and is not expected of humanity. The llamas, too, are not so sure that mankind can follow through, so they’re ready for this to happen again.
I said before that this one is interesting because it doesn’t involve a boat, even though the Incan empire bordered the Pacific Ocean. The Incas were not known as a naval people. Given the roughness of the Pacific compared to the Atlantic, both of which were much rougher than the Mediterranean, too. Also, the Incan civilization favored the highlands of the Andes. Their settlements extended on up to 17,000 feet, well into the mountains. (Incidentally, the highest peak in the Andes is 22,838 feet (Aconcagua), and the fact that the Andes had to grow to keep the water at bay demonstrates just how high the water god in this myth.)
The high settlements make a large degree of sense, especially as the myth describes these high regions as a place of refuge. While the people do descend after the flood, they likely did not descend all the way back down, and stayed in the safety of the mountains and highlands, making this an etiological myth for where the Incas lived.