Asumming the one who wants to destroy it is human too:
here are some ideas:
-a narcisist with a huuiuuuuuuuge ego realizes he is gonna die in a couple of months, so he believes he needs to spare the world from the "misery of living without him"
-out of spite against the gods, maybe he wants to destroy the creation they made because he thinks life was unfair to him.
-maybe the villain is curious to see if it is possible to pull it off.
-to replace them with mind controlled clones.
-to replace their organic bodies with robots with their consciousness downloaded into them, to make the next step into evolution
-Humanity got a rare and dangerous infection and to avoid contaging other living creatures in the universe, they need to destroy the hosts of this disease......humans.
-Maybe they pressed the wrong button at the wrong time......ooops.
-so all souls can go to the afterlife and have a fair judgement going to heaven or hell.