Loop E is what really got me.
If anyone’s interested, here’s the best explanation I’ve seen of everything building up to the Nier Automata. Granted, it’s still Yoko Taro so just be aware that shit’s confusing and plot holes abound.
(Infinite spoilers, don’t watch if you don’t want to be spoiled on Drakengard 1-3 and Nier Replicant/Gestalt)
