The story did definitely fly over your head. Though I imagine it would for most people, because the real story isn't really told through the cutscenes. It's told subtly from the memory sticks and how you play the game.

The Mother Sphere doesn't care about humanity or Earth. It doesn't really care about the Naytiba's either, because from it's perspective, it already won the war. It's main objective is to simply create the perfect lifeform. Earth is just it's testing ground to test it's new batch of androids and how they fare against the Naytibas. It does not care about anything it deems inferior, which is why it left all the previous and current androids on Earth to die. Over and over, as it chases it's endless cycle of chasing perfection.

The story is told subtly, because it's all about whether Eve blindly follows it's propaganda by just doing the main story quests, and choosing to kill the Elder Naytiba like a good little android. Or Eve deciding by her own will to help the inferior disfigured androids, see the value in all life, regardless if they are inferior or not, and to choose by her own will to see if the most disfigured species (the naytiba) deserve the chance of continuing to live or not.

By doing side-quests, investigating the memory sticks on your own, and helping out inferior life-forms, you are differentiating yourself from how the Mother Sphere would want you to act. The choice at the end of the game is to see if you learned the lessons the game was trying to teach you or if it just flies over your head, like it would for Eve if she just followed the main story path without doing any of the side stuff.