Amnesia
What she suffers from

F
ollowing the violent murder of her parents and her own near-death experience, Naoto became afflicted with amnesia. Unable to remember her past or childhood, that tragic night is the earliest memory she is able to recall. There are several different types of amnesia, but the one that seems to best illustrate Naoto's condition is dissociative amnesia.

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Glimpses of Naoto's past from her perspective.
While memory loss in normal amnesia occurs due to injury or harm to the brain, dissociative amnesia is triggered by a stressful or traumatic event, causing the individual to block out information or suppress parts of their memory. Unlike with normal amnesia, those who suffer from dissociative amnesia still possess their memories. These memories, however, are buried deep within their minds and are difficult to retrieve.

In Naoto's case, the traumatic event that caused her to lose her memory was the brutal assault she suffered as a child. Despite nearly taking her life, however, the killer did not inflict any damage onto her head or brain; this indicates that Naoto's memories are still intact—just repressed.

In Dogs: Stray dogs howling in the dark, Naoto is able to recall what happened to her as a child, though her account is somewhat spotty at best.

There are holes in my memory. The only thing that I remember was that I was running away with my family. I don't remember why we were running, or from whom... or even what my parents looked like.
  • Naoto Fuyumine
    Chapter 3: "Blade Maiden [Part 1]"
    Dogs: Stray dogs howling in the dark

B
ecause they still possesses their memories, those afflicted by dissociative amnesia still have a possibility of reclaiming them. Lost memories can either resurface on their own or they can be prompted by one's surroundings.

Although Naoto's encounters with Frühling do elicit some kind of response from her, most of it is emotional rather than anything concrete. Before confronting Frühling for the first time, the rumbling and ominous noises around her has Naoto feeling suddenly afraid. From then on, this feeling of fear resurfaces whenever she is approaching something related to her past.

What's wrong? Why am I so afraid? What am I remembering?
  • Naoto Fuyumine
    Chapter 27: "N & N"
    Dogs: Bullets & Carnage
When her and Frühling's eyes meet, Naoto remembers Frühling as the one who attacked her and her family that night. Aside from the identity of the killer, however, it does not seem Naoto remembers anything new. The scenes that are shown during her revelation are ones that she is already knowledgeable of. What is different now, though, is that these moments of her past are now colored with a greater emotional intensity. The powerful feelings she has towards her past are ones that affect her greatly, causing her to be irrational at times.
H
ow Naoto actually remembers her past is probably not very realistic, but hey! Suspension of disbelief! That's what makes fiction cool, right?

Much later, Einstürzen ascends from the underground, her younger clone visiting the church presumably to take Luki and Noki back "home." When the conversation escalates and Einstürzen threatens violence, Naoto is quick to intervene, drawing out her knife.

Einstürzen: I see you're not beyond threatening a little girl like me with a weapon?
Naoto: If you're the same kind as these twins, then you're the case of appearances being deadly deceiving.
Einstürzen: Oh, so scary. But you know, the same can be very well said for you, too... Fuyumine Naoto-chan.
  • Angelika Einstürzen & Naoto Fuyumine
    Chapter 68: "Mother & Mother I"
    Dogs: Bullets & Carnage
bc068
Einstürzen takes control of Naoto.
With a finger, Einstürzen touches the blade of her weapon and Naoto loses control of herself, turning on her allies and attacking Heine when he returns to the church.

Although it's unclear what the heck she just did, Einstürzen nevertheless releases something of Naoto, causing the latter to become a different person entirely.

L
ater, it is suggested that what Einstürzen did was stimulate Naoto's memory. When she finds herself cornered by Frühling, Einstürzen and Ernst, Ernst compels Naoto to remember what Einstürzen showed her during that time in the church.
My initial guess was a little off the mark. I had assumed you might be another runaway soldier, like Heine. But then [Einstürzen] reappeared before you. What did she show you at that time? Recall it.
  • Ernst Rammsteiner
    Chapter 92: "Sister & Sisters II"
    Dogs: Bullets & Carnage
Suddenly, Naoto recovers her lost memories, and what she sees does indeed confirm her true nature.
O
therworldly shenanigans aside, is it a bit anti-climatic? A bit cliche? It depends. Amnesia is certainly prevalent in lots of fictional works, occurring far more often than it probably does in reality.

At the same time, however, there has to be a reason why it is still used today, despite how overdone it may be. It creates drama and, if implemented the right way, it can create a compelling story. Whether or not the latter applies to Naoto is up to readers themselves. Personally, although I do recognize amnesia to be a common trope, with all the twists and turns the series has taken so far, it ended up not bothering me as much as I thought it would have.

Moreover, although it certainly does play a significant role in her story, Naoto is not defined by her condition. There is a complexity to her character, one that is to be appreciated, I think, regardless of whether or not one agrees with the whole amnesia bit.

References