It’s established that Karda Nui is the “heart” of the Mata Nui Robot, where energy storms rage to give Mata Nui his energy. When Toa Ignika used the Mask Of Life to reawaken Mata Nui, it caused another energy storm that would kill anyone in its vicinity. This was why the Toa Nuva had to evacuate the Av-Matoran and then hightail it out of there.
But wait a minute. If Karda Nui’s energy storms were so dangerous, then why did the Av-Matoran migrate there in the first place? Sure, the energy storms stopped when Mata Nui went into a coma, but it was always the Toa Mata/Nuva’s destiny to reawaken him. Even if the Av-Matoran didn’t know about that, what were they planning to do in the event that the energy storms started up again? Sure, the Codrex was in Karda Nui, but it didn’t need the Av-Matoran to operate anything inside it or perform maintenance…did it?
Looking at human history, it’s safe to say that if there’s place that can be colonized, even if it’s super hostile, someone’s crazy enough to try–and they may eventually succeed. Look at the indigenous people of the Arctic. Why the hell would their ancestors even think that was a good place to colonize? And yet, ethnic groups from Europe, North America, Greenland, and Russia all live within the Arctic circle. For some reason. Same for deserts and other hazardous environments–in just about every biome, there’s people living there, no matter how dangerous it is. Perhaps Matoran are just as crazy and stubborn as humans.
The Av-Matoran originally lived in the cave systems above Karda Nui’s roof. During the Great Cataclysm, shortly after Mata Nui fell asleep and the Energy Storms stopped, the roof of Karda Nui was damaged, and partly collapsed, exposing the Av-Matoran to Karda Nui.
So they basically only migrated to Karda Nui because their original home was destroyed. They also didn’t know about the Energy Storms, I believe.
Gilahu has it accurately. When the stalactites in karda Nui fell, they brought pieces of the av-matoran homes with them. Like the matoran of voya Nui and mahri Nui, the av-matoran were forced into a location that they weren’t supposed to be in, and just dealt with it until the Toa showed up.