Beware: Spoilers Below
Fire Emblem: Three Houses, for the most part, eschews straight definitions of good and evil with the four factions that you can ally with and opts for shades of grey. The exception to this is Those Who Slither in the Dark (Slithers for short). They are outright evil and generally have no real motivation in the grand scope of things, wanting just to kill the last of the Nabataens and then screw over the rest of humanity. While that is the case, it is interesting to consider what the Slithers were up to during the Academy Phase of Three Houses, as during that time, they were working with Edelgard and preparing to attack the monastery. There were plenty of times when their actions made no sense and felt completely out of place.
I was in a discussion with a reddit user named SigurdVII, where he suggested a very interesting theory that we got rather invested into.
So this thread is dedicated to analyzing the overall plan the Slithers had during the Academy Phase.
The first real understanding we get is something that happened after Chapter 4 was completed when the Western Church made an assassination attempt on Rhea, as well as to try and retrieve the remains of Seiros. However, rather than find Seiros's remains (which they wouldn't have found, as Seiros is Rhea), what was left there was the Sword of the Creator. The Flame Emperor would report this to Thales, who was under the guise of Arundel.
Thales was not expecting the Sword of the Creator there (even dropping a hint that Nemesis was just a thief, to the Flame Emperor's confusion), so by some account, the Slithers may very well have expected to have found Seiros's remains, and may not have guessed that Seiros was Rhea at the time. If so, the only logical explanation we could guess was that the Slithers wanted to obtain Seiros's remains because it would contain her bones and her Crest Stone, which would likely be used by the slithers to create a weapon out of it, presumably for Edelgard, who bears the Crest of Seiros.
Remember that Edelgard has no Relic for her own, as Amyr was an artificial Relic created by the Slithers, meaning that Edelgard had no real weapon to channel the power of her Crest. Even Amyr's art shows that it has the Crest Stone of Maurice rather than Seiros. This is the best we can guess for the attack on Chapter 4.
However, the interesting thing came during the same conversation between Thales and the Flame Emperor. The Flame Emperor reports that the Sword of the Creator had no Crest Stone, but Byleth had been able to use its power. This caught Thales off guard, as he states that there's no way that a Relic would even function without a Crest Stone and that even Nemesis couldn't have had any descendants for there to be someone with the Crest of Flames. This is where Thales stops himself and starts to think deeply about something.
It's likely that Thales figured out that if Byleth could use the Sword of the Creator, despite the weapon lacking a Crest Stone, then it must mean that he has or is the Crest Stone. Recall that Slithers have a Crest Stone where their hearts are, as evidenced by Chapter 10 with Kronya.
Now this is where we start to dive into the meat of the discussion
During Chapter 6, after Flayn has been kidnapped, Leonie mentions that Tomas has been asking around about Flayn, but also was trying to learn about Byleth and Jeralt. When confronted, he waved this off about how he's been in the monastery for a long time, and how he never saw Jeralt age, or never knew Seteth had a sister. Sothis later even says that Tomas is definitely fishy.
All of this seems odd, would you not say?
But then you recall what Solon calls Byleth in Chapter 10: the Fell Star. This is no doubt referring to Sothis. Tomas was likely trying to investigate Byleth's origins and figure out if he really was their enemy.
Once you realize this, something starts to make sense.
Ask yourself: Would the Slithers want the Fell Star and Edelgard to actually work together?
And this is the main topic of the discussion we had. It is very likely that the Slithers made all their attacks for the sole purpose of ensuring that Byleth and Edelgard NEVER work together by any means.
It's clear that from the very beginning, regardless of route, Edelgard wanted to have Byleth join her, and, during the Black Eagles run, has been subtly hinting to him and the workings of the Church and how it was wrong. She likely hoped that if she could keep presenting enough information little by little, she could gain Byleth as an ally.
But guess what completely started to sabotage Edelgard's chances of ever gaining Byleth's favor?
During an Exploration during Chapter 5, Tomas tells Byleth that there's a chance that the Western Church attack was instigated by an outside force. This actually makes it clear that there's a mastermind behind the attack. And during Chapter 6, the Flame Emperor reveals himself for the first time, making it clear that the Flame Emperor is this outside force.
But Chapter 8 was the real kicker. In that chapter, Tomas reveals himself as Solon and had conducted horrific experiments on Remire Village, so terrible that even Edelgard is completely taken aback by it. Solon even states that he could have conducted this experiment anywhere, so why Remire Village specifically? Recall how Remire Village seems to have sentimental feelings for Jeralt and Byleth, so much so that Byleth actually expresses anger from the attack.
And after the attack, guess who shows up? The Flame Emperor.
The Flame Emperor immediately tried to salvage the situation by denying any involvement with the attack but was unable to deny the connection they had with Solon before the Flame Emperor made a vain effort to try and get Byleth to join. It makes it incredibly easy to guess that Solon was there to link the Slithers with the Flame Emperor, hence the presence of the Death Knight during the attack, which damaged the credibility of the Flame Emperor for Byleth and Jeralt.
This gets even worse when you recall that after Chapter 6, Monica is brought in, and she sticks VERY close to Edelgard the entire time, to the point that Hubert had to actually force Monica to separate herself from Edelgard.
This is very important when you realize that a chapter after Remire Village, Monica reveals her true intentions and murdered Jeralt. When you explore during Chapter 10 after, there's an NPC student that comments about how close Edelgard and Monica were, and then considers the possibility of Edelgard possibly being involved, before she quickly shut herself up.
Everything starts to add up. The Slithers were actually trying to ruin every chance Edelgard had with Byleth. In fact, Byleth still has a case of considering whether to join the Flame Emperor or not even after Chapter 8 and in Black Eagles, Edelgard does seem to believe that she could convince Byleth to join her. With Edelgard, she even suggests that perhaps that one day, the Flame Emperor would approach Byleth without a mask, with her perhaps holding a faint hope that Byleth can still join her.
But after Chapter 9, Edelgard seems to have more or less given up on ever convincing Byleth to join her. She likely knows that the damage was done, and there was no way to salvage the situation. And even if there was the unlikely chance of still convincing him, the Slithers still tried to make it even less likely by ambushing Byleth when Kronya tried to kill Byleth and after failing, Solon tried to banish Byleth to the dark dimension of Zahras. And once Byleth inherited the power of the goddess, Edelgard definitely felt that there was no way that she and Byleth could share the same path.
Which might make sense as to why Edelgard is so confused and insecure about Byleth joining her when it comes down to it since she feels that there's no way that Byleth would join her in all logical sense.