Unanswered Questions

>There is no reason so far to give Plague the soul, you just miss out on Nae completely and it doesn't effect the story. Pointless and never referred to again.

The game's story ended up a lot different from how I originally planned it, so some of the issues are due to that.
Giving Nae's soul to Plague was originally going to have consequences. She was originally going to be one of the mad bosses you fight later in the game. So it's just a forgotten plot point. Oops.
Also the entirety of the Joki fight is a relic from an old idea. At one point she was going to be the final boss, but I couldn't find a way where that would make sense so she became an optional boss instead.

>What barrier was affecting Llov? We know she's sick because, if we ask Plague, that Llovs "reservoir was destroyed". But we are unaware of the cause of this barrier that Pest mentions.

>We are unaware of who corrupted Nae in the first place and/or destroyed the pylons, although I assume corrupted Nae was the one who damaged the pylons.

Chikungunya was behind the barrier. When you fight her, she can not only prevent you from healing, but prevent you from targeting your allies at all. This is the power she used to prevent Pestilence from healing Llov.
She is also the one behind the corruptions of Naegleria, Rabies, Sars, and Eidzu. When you revive Chikungunya, she mentions that she willingly fell into madness.
Chikungunya serves Mad Cow, who is a very powerful god of madness. The bioweapon goop that's covering the Earth zone is also related to them.
I was probably a little too cryptic about Chikun-chan's role in the story.

In the original visual novel project, Chikun was just going to be included as a joke character, so having her take a serious malevolent role in my game was really funny to me.

>You can’t revive Mal or Pox, and their deaths have zero effect on the story, game, or the characters. Chikun killing them feels pointless and doesn’t add anything.

Pestilence can only revive someone if he has their soul. Chikungunya devoured both of their souls, so they cannot be recovered.
I should make this more clear by allowing the player to interact with their bodies.

>How did Zmapp get into the skull?

Cure-chan put her in there. It was part of their trojan horse plan to resurrect WHO-chan. They needed a lot of human souls to pull it off.

>How did Cure get the skull?

In my original draft for the story, instead of Cure-chan stealing Ebola-chan's skull, there was a weird frog-looking character named Humanity who had stolen Ebola-chan's heart. Ebola-chan was asleep at the top of the tower, and Marburg and Llov had to get her heart back to wake her up.
I don't really have any answer for how Cure-chan got the skull though. I didn't really think about that.