So here's my bigfic idea I'd like to at least start working on.  I don't plan on having more done in two weeks than an outline, but I'd consider that progress.

The plot is this: what everyone who stayed behind in Gensokyo did during the events of Legacy of Lunatic Kingdom.  Specifically, how they handled the Lunarian killbots.

This raises questions:

• The killbots are invisible to youkai.  Who’s able to see them unaided?
  • Are there any ways to mitigate the invisibility?
• How do the locals defend themselves, and with what?
• Which characters will have narrative focus?
  • The series has loads and loads of characters; so too will this fic.

I will no doubt discover more questions as I receive input, and am open to questions from others as well.  

Hopefully this is the right place to brainstorm my idea; I'm unfamiliar with itch fanfic protocol.

Hello. I would like to respond within your questions.

• The killbots are invisible to youkai.  Who’s able to see them unaided?

This means they could be susceptible to other Gensokyo entities, such as fairies or humans, who are not youkai.
A definite answer could be Kaguya and Eirin, who are Lunarian natives.
Another could be the Three Fairies of Light (Sunny Milk, Luna Child, and Star Sapphire). Their combined powers effectively make themselves invisible.
However, their power is not limited to that, since ZUN wrote their abilities vulnerable to interpretation. e.g. "What is manipulating light via refraction?"

• Are there any ways to mitigate the invisibility?

This depends on how you define invisibility in your bigfic. I am no expert on fiction, so you have to do the research. However, as mentioned above, invisibility is not impossible in Gensokyo. There are also different kinds of "invisibility" presented such as Sakuya time manipulation and Nitori's optical illusion. Just like ZUN, if you can make the character's abilities work, then this question gets resolved.

• How do the locals defend themselves, and with what?

As far as I know, there is no defending to be done in Gensokyo. Usually, a higher power would send off their hypercompetent incident resolver to do the work for them. The Human Village is never involved in incidents because entities like Keine and Akyuu wont allow it.  Ultimately, if your version of Yukari Yakumo deems these killbots a threat, then she'll personally interfere or pull some strings to get other players on the field. This may be left to your interpretation as the author.

• Which characters will have narrative focus?
  • The series has loads and loads of characters; so too will this fic.

Personally, it feels rough to suggest characters for someone else's idea. Everyone's idea of Gensokyo is different, so if you want a character to take more of an initiative then you're free to do so. If you want a character like Rumia to take the spotlight, then by all means. 

I hope these responses were able to answer your questions.

• This means they could be susceptible to other Gensokyo entities, such as fairies or humans, who are not youkai.

Of course; fairies, humans, gods.  Which Byakuren says youkai may as well be, but I'll need to figure that more pending suggestions.

• This depends on how you define invisibility in your bigfic. I am no expert on fiction, so you have to do the research.

Noted.  Time to put my degree to actual use then.

• As far as I know, there is no defending to be done in Gensokyo. Usually, a higher power would send off their hypercompetent incident resolver to do the work for them. 

Except in LoLK they kinda busy on the Moon, and I don't think most warbots play with spell cards.  And the Lunarians wouldn't send things that Yukari could gap away.  What was she doing then?  Something else up for creative interpretation, and work on my part.  But I'm always open to suggestions.

• Everyone's idea of Gensokyo is different[.]

Oh yes.  I go more for character development and worldbuilding, with a modernist and practical focus.  In contrast to the more common jokes and shipping, and what I can politely refer to as not letting common sense get in the way of taking it easy.  : p

• I hope these responses were able to answer your questions.

Technically no, but they do provide one starting data point for my intuition so it's useful all the same.  Thank you for your thoughtful response.  : )