I said I wasn’t going to do this but I changed my mind. In general, I prefer discussing broader ideas over specific predictions, so this will more be that with a discussion of possible derivative theories. Note: there are some Xenosaga spoilers.

MTSC and Gilliam Thornedyke are the main villains. 

I’m not the first person to propose this. MTSC has been a suspicious organization since they were first shown in Hajimari. You have a private military contractor that pops up out of nowhere having Ouroboros level technology including advanced AI, full body prosthetics, and powerful weaponry while working with the new Calvard president to implement an Ouroroboros tier plan of their own. On the surface, this isn’t much different than the relationship between Osborne and the Gnomes, but the Calvard arc so far has generally been a thematic inversion of the Cold Steel. It make sense that the roles would end up reversed. More importantly, the real reason that MTSC must be the main antagonist organization is that they are the only organization that serves as a foil to Arkride Solutions. 

In every arc, the main antagonist is the leader of an organization that is superficially similar or adjacent to the protagonist’s in terms of philosophy, structure, objectives, etc but with some clear differences that makes them wrong and the protagonists right. In most cases, they are allies to the protagonists in the first ‘act’ before taking the role of antagonist in the second. For example Bracers and Ouroboros are similar organizations in that they give their members a lot of autonomy but in Ouroboros’s case it’s false autonomy due to the underlying darkness (and Weissman straight up breaking the rules). In Crossbell, you have police versus the government; both want to free Crossbell but the government is doing so in a way that’s just going to create more barriers. Erebonia then has school children versus Osborne’s Ironblooded Children—groups made up of similarly exceptional and promising youths. In Kuro, both Arkride Solutions and MTSC are gray organizations that take on work involving the intersection between the surface and underworlds and often have similar employers.

Furthermore, there are a lot of contrasting features between Van and Gilliam Thorndyke:

• On the surface both seem to only care about the money and treat everything as transactional. For Van, this is mostly just an excuse to convince himself that people are distant. Gilliam seems to only care about himself.
• Van comes off as unfair because he charges more than the guild, but can actually be quite lenient depending on the client. Risette says that MTSC is a very fair company to work for.
• Van comes off as a dick but is actually a nice guy. Gilliam comes off as a nice guy but is (probably) a dick.

Additionally, someone at Falcom is heavily influenced by Xeno- games considering how much CS was influenced by Xenogears. MTSC and Thorndyke seem like obvious proxies for Vector and Wilhelm especially with Ouroboros’s plan being the “Eternal Recurrence plan”. 

Derived Predictions

• Most enemy factions will end up being connected to MTSC in some way or another whether it be Heiyue’s Lai family, Zecht Arms, Garden, etc. 
• Garden Master (Ace) was saved by MTSC after allegedly being killed by Swin. His current body is mostly cybernetic like Risette’s. 
• Altera is an AI based on the data collected on Van’s Hollow Core. 
• Gilliam is a timeless being able to retain his memories or even entire existence across multiple loops. He’s either one of the 5 Demon Lords, the Holy Beast of Time, or unshackled like Epstein. 
• Gramheart was a red herring. Kuro in general has been an inversion of the Erebonia arc, so MTSC betraying Gramheart is not out of the question (and also like Xenosaga).

The Holy Beast is a humanoid

Going by the children of Loki theory, the last holy beast of the higher elements should be a humanoid. I don’t know what Falcom is doing but I’ve assembled a bunch of possibilities. Note that these are not all mutually exclusive.

• 1st of the 5 Demon Lords, Hel was the Queen of Hell and the time element has a very demonic feel to it. In Ars Goetia, the hierarchy of Hell was Lucifer, the four lords, and the remaining 72 demons. Lucifer was a fallen angel so maybe this is the fallen holy beast. Maybe they are female to reflect that YHWH’s gender was changed to female with Aidios.
• Gilliam Thorndyke, the purpose of the Holy Beasts is to observe the fate of each of the Sept-Terrion in the hands of mankind while maintaining a position of neutrality which would be easy to do from a neighboring country. You could argue that only caring about money could be his way of maintaining neutrality (though I think this conflicts with him being the main antagonist). 
• Nina, she is sus in general so I’ll just put her in every list.
• Hermes!!! She seems like a deliberate reference to Celty from Durarara who was a Dullahan—a humanoid monster. I wrote in my earlier theory that the Sept of Time is supposed to already be lost which would make her contract already complete. There’s also the question of why she, a random delivery driver, is involved with Gramheart’s space program.   

Host and Devil, Chicken and Egg

It seems obvious to me that the 5 Demons Lords is a plot device introduced exclusively for the Calvard arc. Vagrantz-Zion has power over time, they didn’t exist until the world was reset at least once, and structurally they appear identical to Erebonia’s divine knights. My big prediction about them is that they were originally human—in fact all the 77 Devils were (read my other theory),—and in future timelines, they are always the same human. In other words, Vagrantz-Zion is the culmination of all the memories of all past versions of Van Arkride through the infinite number of times the world has been rewound and reset. He says as much; Van Arkride is a part of Vagrantz-Zion and will eventually become him. The same is true for the remaining four.

Related Predictions

• Death is the key. All five hosts had a near death experience which connected them with their corresponding devil. 
  • This is why Garden Master acts so much differently than Ace. Upon nearly dying, he merged with a millennia of memories of all different versions of himself. Imagine yourself as a six year old suddenly gaining the memories and experiences of yourself now. It would completely change you. Now do the same but with thousands of years of experience. 
  • Van Arkride managed to avoid this fate by having his diabolic core removed by the cult.
• Candidates
  • Elroy, his concept art makes him seem based on the Joker who broke after losing a loved one. Seems like what Van could become after experiencing losing Elaine enough times.
  • Gilliam Thorndyke
  • Garden Master (Ace)
  • Gouran, because why else would they introduce a new rival character.
  • The Twins, just throwing it out there.
  • Nina because she’s sus.

I refuse to make any predictions about Grendel-Rojo other than he’s not Van-Alter and he’s not Vagrantz-Zion. His form in Zolga’s S-craft is too different.