So that is the horrible truth behing everything in Nausicaa's world. She has committed herself to fighting on the side of the "natural" world, only to learn that there is no natural world left! The world of the Ohmu and the regenerating forests are as man-made as the God Soldiers and the technology which destroyed the world in the first place. And worse, all the humans alive in the world now are artificially modified to endure the polluted world. None of them will survive once the world has become cleansed again. After she has escaped from the garden and she is preparing for the final leg of her journey to Shuwa she thinks back to the old Holy Emperor going off with the Hendra on what he thought was a noble cause. Just then Kesh, one of the creatures from the garden (who looks a lot like Yakkul from Princess Mononoke), comes to her camp from the garden to return the clothing she left there:

Now I tread the same path with the wormhandlers and the God Warrior....For all I know, I may be going to destroy humanity. And that is exactly what she is going to do one way or another. When she reaches the Crypt, she discovers that within it are the seeds to bring about the rebirth of genetic humans from before the Seven Days of Fire who will be able to live in the newly cleaned world. Both both the old humans and the new humans cannot live together in the same world. Does she throw her lot in with the pre-Seven Days of Fire humans? After all they are more"natural" than she and her world is. But of course these are the descendents of the people who nearly destroyed the world in the first place. Should they even be given a second chance to destroy the world completely? Or does she throw her lot in with the "natural" world as it is now, with all the humans now living? Of course, if she destroys the old humans, it's just a matter of time before new humans like herself die out completely as the forest complete their work of cleansing the world. So this is the painful, no-win choice that she must make, which part of humanity is she going to condemn. Which "natural" world will she ultimately allow to survive?
I won't tell you what she finally does. It takes the last half of thelast PC volume to explain that, but I will tell you that it's a decision thathas had Miyazaki's fans going around in heated debates about it since the final installment was published in 1994.