This is a theory I thought about the other day after finishing the 2.5 event, Showdown in Chinatown (so if you haven't finished that event, click out if you want to avoid spoilers), but before I fully explain it, I'll give you some context.
In the first stage of Chapter 3, we're introduced to SPDM with a teacher asking the kids about the war between humans and arcanists that happened in Constantinople. First, Sonetto gives an answer that pretty much puts all the blame of the war and the eventual result (the arcanists being defeated) on the arbitrary and violent nature of arcanists. Then Matilda interferes with information that was provided to her by her grandpa.
Matilda's version of the story is pretty much the opposite to Sonetto's; the humans ransaked Constantinople to gain access to the literature of arcanum, and then isolated and blamed arcanists, forcing them into hiding.
Although the truth is most likely somewhere in between, you can probably see that Matilda's version is more in line with Manus Vindictae's way of thinking; humans have been marginalizing arcanists for centuries and stripping them from any position of power (although of course the Manus use this as an excuse for revenge, which Matilda never suggests). More so, it hints at Matilda's family knowing something about the origin of the name "arcanists", which I wouldn't be surprised if it has something to do with Arcana herself.
Now, what happens next? The teacher inquires further to see what else Matilda can tell them about this version of the story and the song it came from, however, strangely enough, Matilda can't remember anything else.
She even goes as far as remarking how weird it is, since she had been humming it just the night before. And it's not like Matilda usually has bad memory; being the third best student in the school, she's bound to have above average memory, so it's even stranger that this is happening to her.
Now, my first assumption (and I most ppl's probably), was that the Foundation was brainwashing the kids and making them forget the outside world... but that's not the case; all of the kids Vertin asks later on remember at least something from their life before joining SPDM. More so, I always saw it as a plothole that the Foundation could erase memories, but then didn't do that to make the kids (or at the very least Vertin) forget about the disastrous parade ceremony, that even Constantine admits was a bad move on their part.
I even thought maybe the whole artificial sonambulism they put Vertin through might have been to, not only keep her in a coma, but also to erase whatever bad memories she had of the foundation and therefore make her more obedient. But as we see in the Tuesday's event, Vertin clearly hasn't forgotten about her friends or how they died.
So... what caused Matilda's memory loss then? Well, the answer is simple: her mom. Hear me out.
During the 2.5 event, we learn that Scott stole and sold 5 arcane items from the Foundation's archives, but her motivations and her methods seem very suspicious, so Black Ibis, a member of the Vigils, keeps her under surveillance after they're unable to learn anything by interrogating her. And this vigilance pays off; she is soon contacted by none other than Matilda's mom.
By the looks of it, Matilda's mom is able to hypnoptize other ppl at a distance (we don't even know where she is), and contact whoever she wants by the use of crystals. She can also lock memories of ppl to prevent any information she doesn't want to fall into someone else's hands from being retrieved. That's what she did to Scott... and to Matilda too, probably.
Listen, Matilda's mom is very suspicious. Black Ibis mentions that one of the items stolen could perhaps be used for "that ritual" (probably Arcana's resurrection), and so whoever stole it likely has that as a goal. However, it seems she's been pretending to be in the Foundation's side all this time, to the point she sent her daughter to SPDM and she herself was staying at a Foundation's safe house. But of course she's highly intelligent and talented, and so, to prevent any sensitive information from being found by the foundation, she locked some of Matilda's memories, just in case the Foundation would try to pry into Matilda's mind.
Matilda very likely even knows where her mother is, but that memory is locked. If her powers were more developed, however, she probably would be able to break this barriers and find her. At least that's how I interpret what her mother said to Scott.
But why lock the memories about the song Matilda's grandfather used to sing? Probably because the song, somehow, is associated with Manus Vindictae, Arcana, or some other group that the Foundation deems as dangerous. Remember that Matilda comes from a long line of pure blooded and extremely talented arcanists (as is explained in her first bond story); exactly the type of arcanists that would be most likely to be approached by the Manus.
In any case, I hope we'll find more about this in the future. Let me know what you think!
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