Casual reminder to lore police that “loyal to the Dominion” is extremely abstract and can be worked around, both in-universe and out:
There is at least one Mechari serving House Chaul, the secret seventh Luminai house that (for reasons yet undisclosed) is so disgraced that no one ever talks about it and the history books were essentially re-written to exclude it (this is assuming that House Chaul is a “true” house, descended from one of Dominus’ children. It’s implied that it is, but that would mean Dominus had seven children rather than six, and the whole Vigilant Church is built around the six Scions. That would be in keeping with the game-wide theme of “six important things, but then it turns out there’s a secret/forgotten seventh thing”, but it would still be pretty extreme. I digress.) Mechari aren’t supposed to be associated with House Chaul at all, and the one that is implies that he’d be in a huge amount of trouble if he’s found out. This is treasonous, but he does it anyway. This sub plot can be seen in Deradune, in the Firewalker area.
Agent Lex is unique in many ways, one of which is implied to be the ability to go against the wishes of the Dominion as a whole. Specifically, he is loyal to Axis Pheydra. His story implies that Mechari may have a sort of Three Laws thing going on that prevents them from killing the Luminai, but Lex is capable (and has done so at least once) because of the modifications Pheydra did. Granted Lex is unique…but Pheydra is not, and she’s the one that started the whole thing. Pheydra is “just” a Millennial, the same as every other Millennial in terms of being loyal to the Eldan, and yet she has no problem following her own path, including making sure no one, not even a Cassian or Luminai, gets in the way. This implies that whatever safeguards the Eldan may have designed, they aren’t absolute (which actually would be in line with the earlier Three Laws concept - Isaac Asimov wrote at length about how even absolute restrictions don’t remain so in real situations!) See the above mentioned Deradune questline, and the TFBTF story “A Test of Loyalty.”
Everyone points at C.o.G.S., but that’s because it is relevant: Technically, by the Dominion’s usual reckoning, C.o.G.S. is an enemy faction simply because they aren’t specifically allied with the Dominion and they are on friendly terms with the Exiles. Yet there are many Mechari in it, because they can “get around” the loyalty thing by reasoning that their discoveries and work, which are shared evenly with everyone, will benefit the Dominion. I cite this because it means Mechari “loyalty” isn’t that hard coded.
Mechari are loyal to the Dominion, but what does that mean? Is it upholding the word of the emperor? Is it insuring the welfare of the people as a whole regardless of anything else? Is it following the path of the Eldan?
There’s also this side point:
Technically the Cassians were simply allowed to live, they don’t actually have any claim to anything of the Eldan’s. Even the Luminai are more like stewards, meant to extend the Eldan’s power and influence once the Nexus Project was completed. Things just didn’t quite get to that point…If we ever get the Coralus zone this will be expanded upon a bit, but if you’re a Scientist you can get some really interesting information about how the Eldan learned about Cassians in the first place from a scannable data node in Wilderrun (which can be seen here, though bear in mind the post itself contains speculation). The Millennials probably know that, and even the Initiates tend to think of themselves as being the real superior ones. In line with the above mentioned vague nature of what “loyal to the Dominion” means, it wouldn’t be a big leap for a Mechari to take the reins in a more forceful manner than usual. After all, the Eldan predicted that the Luminai would become mentally unstable over the generations (see datacube in Auroria) and they’ve certainly made a royal mess of things in the last few hundred years…
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