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The first assumption I'm going to use is simple: everything we've seen in a manga panel is legitimate and canon. Whether I trust Nanachi or not, if the author of MiA illustrates it, it happened. There's not enough data to work with if we discount Nanachi's entire backstory, like half the contents of Episode 13.
The key here is unravelling the gaps withing the visual narrative. Suspicious timeskips within a flashback sequence, with our only data being Nanachi's words, is where we will fill in the blanks.
Let's start with facts that even those who disagree with me will agree with:
Nanachi's entire narrative pre-blessing is accurate (this is the largest change from my original theory)
Bondrewd turned Mitty into a blob used her to give Nanachi the blessing
Nanachi took Mitty from Idofront and went to layer 4
Nanachi continued running cruel and painful experiments on Mitty
Nanachi claimed she rescued Mitty from Bondrewd's cruel and painful experiments
Next, the relevant timeskips post-Blessing
Between gaining the blessing and seeing Mitty exploded
Between seeing Mitty exploded (but still having both eyes) and "rescuing" her from Idofront (with only 1 eye)
Various moments during human experimentation in the hut
Next, the basis for my questioning of Nanachi's narrative. Nanachi is a highly manipulative character. Her words are finely crafted to make people dance for her. It seemed innocent in L4, when she convinced Reg to do some menial labor. But her manipulations were not so in the past. Nanachi admitted to Riko that she manipulated the children in Idofront to make them more willing to submit to the surgery.
