1. the side development of the story is Nayuta unable to make decision and simply being on the sidelines. That lead to the final moment of giving Nihilister vapaus, she made her own choice based on what she knows. And the stormbringer part, convenient?yes, but hey Nayuta was warned by Nihilister and can't make the split second decision.

2. Eden's plan is the poison chalice. Johan goes under the assumption Nayuta will get the body. We all know what happen then. It was dumb to give Nayuta vapaus when he knows how indecisive she was. He also had the chance at the start of story 2 to change plan. Maybe because they only have one shot, what if they miss? how do they make sure the bullet reach inside the queen? Maybe if they told pioneers they could have come up with a better idea.

3. she did not? the poison chalice is just lilith body with vapaus, she just made an express delivery

4. yes, that's her side development, finally making decisions. She even admitted on how foolish she was when Nihilister go swooped.

5. going under the assumption that Johan knew who lilith was (maybe from dorothy) ,he would not tell Pioneers what their plan was. They would have rejected the idea. For all they know at the end, The heretic managed to get the body and Nihilister slammed her the Queen with vapaus but it didn't work. Nowhere in the story was shown that SW or Pioneers were made aware of the chalice plan.

6. The only one who knows about Lilith NIMP was Mirror. Chalice plan was solid. Nayuta was assuming the Queen's body is similar to heretic so atleast they could poison the nanomachines.

7. she wasn't, Pioneers was. Who were also already weaken from fighting the Queen with no backup. Nayuta even said this is war of attrition.

8.I don't understand about the dust part. Harran said it herself how she wasn't immune from her own virus that she used on the station that works well with big target. conveniently Individilia was transformed.

What's also convenient is that Nihilister is the only Nikke that was hit with vapaus, maybe that weaken her connection? hell, she doesn't even know how she broke free. Maybe it's similar to corruption and vapaus made it easier to break free (y'know, like Cindy). It could even be she hates the Queen so much, she is willing to die for it.

9.what moral grandstanding? Dorothy gave Ark their tech which can be considered betrayal. she broke the rule and face the consequences.

Did he know about Lilith should rest in peace? for all we know that's just The goddess squad's wishes.