The Stone-Like wiped out all life on Earth, right, save for our plucky little group of survivors here. However, after a year, they have to come back down to Earth to get some food. Most if not all food was once living matter, and the Stone-Like wiped out all life, not just the humans. So, in other words, there would have been nothing to come back to, and if they returned to the ship without confronting the Stone-Like, they would have eventually starved to death.
Also, most of the soil is made of decomposed living matter as well, which would have been destroyed along with everything else. No wonder the cities and what have you are in ruins; their foundation's completely gone!
Given the Downer Ending and the revelation of a Stable Time Loop in effect, just how many times has the Stone-Like destroyed humanity? As per the C.R.E.A.T.O.R.'s words, "countless"; this includes the fact it has revived mankind repeatedly through cloning. Furthermore, C.R.E.A.T.O.R. muses humanity will "lead the same lives without considering the consequences" before it shuts down, implying it's guaranteed to happen again. It's certainly an Understatement when players state Treasure crafted an exceptionally dark and depressing story out of a Shoot 'Em Up.
