Det är inte förklarat. Det närmaste vi får finns i Vonda McIntyre novellisation . Det var något att göra med tektonisk instabilitet
"You lie!" Chekov shouted. "I saw the world we left you on! It was beautiful; it was like a garden—flowers, fruit trees, streams … and its moon!" Chekov remembered the moon most clearly, an enormous silver globe hanging over the land, ten times the size of the moon on Earth, for Captain Kirk had left Khan and his followers on one of a pair of worlds, a twin system in which planet and satellite were of a size. But one was living, the other lifeless.
...
"Alpha Ceti VI, our beautiful moon — you did not survey that, did you, Mr. Chekov? You never bothered to note its tectonic instability. It exploded, Mr. Chekov. It exploded! It laid waste to our planet. I enabled us to survive, I, with nothing to work with but the trivial contents of these cargo holds."