The way I understand, the author just laid out endgame spoilers without the midgame context that leads up to it.
This is the matrix but it either all hinges on makoto (everyone is connected to him specifically), or it's designed to make every person feel that way. Words like "Error" and "Bug" imply this world is digital in some capacity, or at least powered by machines. She even used the phrase "
cutting edge technology".
@Tamerlane
This is the matrix except Agent Smith comes out to tell you that he
gave you the fucking red pill and
now he's taking it back.
It still makes no sense.
Also I feel like the author referring to Yukki as "having a sexual role" is too much of a reference to the audience's view of her than her actual role in the story.