Well... that is a thing.
I like where this is going, though poor Nepgear is really getting the short end of the stick. She's just started to get used to a peaceful world, is still plagued by nightmares and hallucinations of her guilt, and then... boom. Plot happens.
Though, on another note, I can't say I'm partial to the idea of Planeptune citizens being all reverent towards their goddess. For one, because Neptune definitely isn't the kind of person to encourage that kind of behaviour, at least not outside of a few practical jokes perhaps, but also because I'm pretty sure that I remember quite a few chirper events and story events where both Neptune and Nepgear interact normally with their citizens.
Just a personal bugbear, but it doesn't affect my enjoyment of the story.

It's here, too! I really hope this means you're getting back on this bandwagon, because on a re-read, this is still amazing. I just really want poor Ge-Ge to be okay...
Carry on, Guardsman.