The EVE Protocol is a master plan created by Mother Sphere to wipe out the Naytibas.
Members of the EVE Defense Force are sent to Earth from the Colony as part of this plan to combat the Naytibas that dominate the planet and eliminate the Elder Naytiba, with many believing that the EVE Protocol’s ultimate goal is to reclaim the planet for humanity. However, upon the discovery that not only is Mother Sphere actually a highly-advanced artificial intelligence created by humans, but that all the “humans” living in the Colony and the city of Xion are actually androids called Andro-Eidos and that the Naytibas are the mutated descendants of the original humans, the EVE Protocol is revealed to be Mother Sphere’s ultimate plan to completely wipe out the human race and claim Earth for the Andro-Eidos.
Whether or not the EVE Protocol succeeds depends on what ending is achieved based on EVE’s choices at the end of the game.