I think I can field these questions. WMD, Ascension are in a state of constant enhancement, so the permanent implant could be a future development. Also, I personally think it would be better if you went for the second story idea, she used to work for Ascension but left for one reason or another. This could explain why she has been absent up to this point, but it is up to you.
prs, why should they want to nuke the whole place? That is counter productive in any warfare situation unless you are planning on complete annihilation. Ascension aren’t after the land only, they’re after the people as well, and you can’t really get hold of the people if they are dead.
It would probably help out people to add me on Facebook, me, Iscarioto and Alex of Limbo have been brainstorming major plot developments and it would probably help people out if they are wondering about stuff like that. PM me and I’ll send you a link.