My issue is I don’t know how I would write any more of the alien and probes without it being filler or causing issues with other plans. I don’t want the aliens to show up for a long time (maybe books if I get enough momentum going and ideas on virtual paper). First comes sickness, death, civilization collapse. Then survival, experimenting with powers, rebuilding and “questing”. I’m going for a more magic from technology vibe without anyone knowing it until rebuilding or maybe a mad scientist discovers the nanites as technology is required and most tech is taken out. Maybe time to rewrite some of the plot to fit the altered prologue and flush it out as well as cut it up. Give me a day or 5 to come up with a reworked version 2 for you