The Sith assassins are like miniature versions of Meetra (the Exile) and Nihilus, non Force Sensitives that had what small connection to the Force ripped away from them when the Mass Shadow Generator wrecked Malachor V. This makes sense of how strangely inhuman they seem, and their ability to track Jedi despite not displaying any explicit Force powers. This also gives them more parallels to the shadows in Planescape Torment. Finally, it puts Atris’s line that “These Sith come from you” into sharper relief. And while we’re on the subject, let’s that talk about that line….
Malachor V is the real villain of KotOR 2, and the Sith Triumvirate are its unwitting agents. Looking at the party, Nihilus has a major impact on Visas and is the Exile’s vision of what could happen to them, but doesn’t really intersect with the rest of the party. Sion is their initial threat, relates to Kriea, and gets a fixation on the Exile, but he’s ultimately not much of a personal enemy to the party. Traya is their initial threat exception to this trend, as she messes with everyone, but is still ultimately tied much more to the Exile than anyone else. However, many party members have some kind of link to Malachor V, to the point when it’s time to go there, it’s the planet that freaks them out rather than the Sith on it.
Thematically the game revolves around wounds, how they spread, and how they’re healed. Lightside options are about healing, especially in regards to how the Exile relates to the party members, where the player heals the people and places they come in contact with and cause them to become agents of further healing. Darkside options are about ripping the wound further, making those people and places agents of further harm. Malachor V is presented as the ultimate wound, in the very fabric of the Force itself, and if you look closely at the Triumvirate each is an agent in some way of spreading that harm.
Darth Nihilus is the most obvious, throughout the game he’s presented as a walking force of destruction more than a person. He sucks out the Force wherever he goes, feeding on it but ever hungry. If his origin is on the destruction of Malachor V, which I think is the most implied, then he’s ultimately a force for spreading the wound.
Darth Sion might be the loosest thread in this theory, as there’s fewer things you can point at to say that he’s serving the planet. However, he does always comes back to it despite there not being a sense that he strictly needs to, even if that means submitting to Traya, a fate he sees as so dismal he’d kill the Exile to spare them from it. As someone addicted to the suffering he must endure to stay alive, he can’t seem to quit the place that represents the ultimate suffering.
And for Darth Traya, a.k.a. Kriea, as the winner of the Triumvirate’s leadership struggle, she seems like she’d be the big bad of the story, but I think something doesn’t add up. Her stated goal is the death of the Force, but she’s not completely consistent with it. Kriea’s not exactly disappointed that the Exile stopped her, and in the following conversation she seems less hostile to the Force than she was before. This could mean that saying she was trying to destroy the Force was just a cover she used to force the Exile to fight her, but I have an alternate theory. When Kriea describes what it’s like to feel the Force to the Handmaiden, her account sounds wistful and nostalgic, not exactly hostile. I don’t think she necessarily wants to hate the Force, thinking of this speech in light of the ending makes me think Kriea’s relationship with the Force is more like a disappointed former friend than a bitter archenemy.
So, this might be the most speculative part (if any of this was explicit it wouldn’t be a theory), but I think that Kriea is getting caught it the Malachor Force wound’s spiritual gravity. Her negativity through the Force is being fed beyond its original state to aid in the Force wound’s ultimate spreading of its infection. Seeing how far the Exile has come, and how they can bring in something new to the galaxy, gives her a moment of clarity, and she can finally be at peace.
So “these Sith come from you” doesn’t mean the Exile created each member of the Sith Triumvirate, there’s nothing that suggests that. But she created their source and motivations by using the Mass Shadow Generator on Malachor V, which turned it into the ultimate wound in the Force.
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but left it anyway as WW1 was pretty much the last hurrah and final collapse of the 19th Century empires and sensibilities. 
