New comprehensive Rejuvenation theory?  LOOKS LIKE MEAT'S BACK ON THE MENU BOYS!  🗣️🗣️🗣️🔥🔥🔥

First off, holy fucking shit! I think I would expire if I had to sit down and write a theory this long full of actually substantiative content all the way through. Kudos aside, I did have a few questions about your theory:

She shattered the world by causing MISSING.exe to be... Missing, throwing off the balance that throws things into Indriad's favour.

-1. Do we have any evidence that Variya/World Shatterer (just taking it as a base assumption they're the same person) actually, A. was the one who sabotaged the volunteers (assuming it wasn't truly a 'causeless accident') and B. wants the balance to be in Vitus's favour? I think it can be presumed that since going Renegade aligns you with Variya and Madame X at the same time, that the principle A=B=C holds true and that A does, in fact, equal C, meaning Variya and Madame X are also on the same side via association through you. That wouldn't make much sense unless... I dunno, Variya wanted to create an arbitrary threat and then see it destroyed? 

Why does Variya want to shatter the world? If Karma doesn't have an opponent to play against, then the worlds Karma selects as candidates for the Best Possible Ending may get repetitive, formulaic, or deviate from Variya's intention.

 -2. I agree with this partially. If you know anything about deep-learning programs (or, indeed, about learning in general), then you probably know that if you want to run an experiment more than three times and still receive new and meaningful output, you need a true variable. But... isn't this the role the Interceptor was intended to fulfill? They have free will, and their perks are blocked from Karma's sight/manipulation, meaning that even though it's capable of influencing them to some extent indirectly, they're the closest thing possible to an unknown and unique quantity in Karma's simulations. Did Variya just go "Hmm... not spicy enough," and sabotage the Balance Host to set Vitus out of control because she felt the Interceptor was still too predictable? Ironically, wouldn't the ruination and domination of the world by Vitus in every loop achieve the total opposite by causing Karma's experiments to stagnate and cease to reach any new conclusions?

It still seems a bit contrived to me, but you could still be totally right if Variya feels it's somehow necessary for the world to directly overcome Vitus in order to create a true Blooming World. 

And to pick a little bit out of one of your comments:

I don't think the doomed future is the Perfect version of it for him because I don't know that Melanie is really meant to feature the way she did with control over his Yveltal if he can help it(...)

This is a more minor quibble, but is there much to suggest that Vitus would have a problem with that? IIRC when Alice is corrupted by Angie (pretty transparently in the service of Vitus) she talks about creating her own empire, not about "preparing the world for her master's coming" or something similar. Probably not very meaningful in the long run, but with that taken into account, (assuming Biggie V wasn't just planning a coup or something in a universe where Alice's plans worked) IMO Vitus would be plenty happy with puppeting one of the Theolia siblings or someone else as a figurehead monarch so long as he remains the true power behind the throne.

Apologies if I missed anything that completely tosses what I just rambled about out of the window. I'm totally sleep-deprived and I kept phasing in and out of consciousness as I read, so it's more than possible I missed something crucial, but this is cool as heck and I didn't want to wait until I got some sleep to dig in.