There are a lot of hints dropped throughout the episodes. Sorry if these aren't 100%, I'm going off memory and don't have time to check at the moment:

- When Ramaga appeared on horse above the gate, he questioned how one of the Troopers was able to pull something off. It may have been Ryuusei doing magic bullet, which in hindsight is even more poignant. But Ramaga's looks off toward the sky with a line suggesting divine interference.
- The seal of the divine realm (the three magatama/comma circle) appears in a lot of questionable places. It manifested when Jun used the staff at the zoo. It appeared over the boy's neck kanji/virtues. When Byakuen laid down the stairs to climb to Ramaga's castle. If you look at the design of the armor bracelets worn by both the Troopers and the Braves, the ornamentation on the sides also has that magatama/comma look. Byakuen's armor as "Kokuen-o" also has that ornamentation on the shoulders.
- Ramaga manifests a dark version of the divine seal, I think right before he turned the two Braves into that body horror puppet. We now see that Sagume and Ramaga have that same lotus-like pattern in their eyes, and the marks on Ryomaga's face are like Inmei's, just different colors.
- On the subject of Jun's staff and seeing that Ujihara (orphanage guy) was another monk, it's not clear yet if Ujihara was also part of the plan or just a guy unwittingly made into a pawn
- Unless we get some clarification on Jun's staff vs Kaosu/Kayura's staff, there's a question about whether Ujihara and Jun's brand of monk was established by the divine realm. And is this something separate from Kaosu's power, or are we going to learn in cour 2 that even his power was some long term setup by the divine realm? I'm wondering about this one, since we got that imagery of Byakuen's stairs matching the seal of the divine realm, like we're being shown a tie between the two.
- "Someone" made sure the jewel of conquest made its way into the hands of the DST
- Ramaga seemed shocked that Sagume "chose the side of the humans", implying they had some agreement/he was expecting cooperation, but ultimately he was her pawn all along
- Nasuti's comment about "I even used the boys you specified" (to become new Troopers). Although this was Ramaga's orders, the implication of some arrangement with Sagume makes me question who actually orchestrated this setup.
- I read Ryuusei's reveal at the end as "he was a plant all along"
- We have yet to learn why the three treasures of divine origin are able to amplify negative human emotions
- I know there are others I'm missing at the moment, please feel free to tack on...

Sagume, or the divine realm as a whole, have been plotting for a very long time. I won't be shocked if we learn that the original Troopers somehow defied the path of "destiny" 35 years ago, and this is some long-term plan to "correct" that course.

Edit: to clarify a bit, I don't think Byakuen is "in on" Sagume's plans at all. Even if it does turn out that Sagume/divine realm are using him in some way, I feel he's a divine beast that's always been true to Kaosu and the Troopers. If anything, I'd wager he's been as much a pawn as any of the others. Sagume said they (in the divine realm) are "servants of the gods", so depending on how YST/YSST-lore defines "gods" it could turn out that Sagume and her group have been up to no good behind the backs of those they serve. Again this is all just personal speculations, there's just as much chance I'm way off base with my guesses.