I've been trying to piece everything in the story together, but now I'm starting to find a lot of inconsistencies. So spoilers for all of the main games shall follow. Actually, I don't know about Episode II. I don't think there's any inconsistencies in there, so yeah.
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Most of the inconsistencies/questions are because of Chapter 6/7. So you can guess what most of them relate to.
First, a few things with Virgil. As I brought up before, how did he get to the church if there was nobody there to save him from the soldiers? I can only think of Febronia or Federation soldiers even attempting to save him. I doubt Febronia would have succeeded, and why in the world would Federation soldiers take him to the CHURCH out of all places? So neither of those are likely. I don't have any other logical ideas.
When EXACTLY was Virgil supposed to have started eating the Realians, and why did he eat them in the first place? He stated in Episode I that he was looking for something, and found the control code by accident. But, you know, the control code can't have existed at that point, because otherwise the entire berserk Realian thing could have been fixed by using it.
The only thing I can think of is that the Song of Nephilim actually overrides the control code. But nothing of that sort was ever said, and that's a pretty important thing, so that would be weird. And that still doesn't explain what Virgil was originally looking for.
What would have happened if Shion hadn't been there to give Virgil the control code? Because him blowing them all up did not actually happen. Without Shion's interference, it would impossible for him to obtain that code. Especially since it doesn't exist at that time.
It's possible that he stayed behind to fight them and ended up eating them at that point, but unless the Song of Nephilim DOES override that control and it DID exist at that time, it's inconsistent with Episode I. And again, why would he start eating them if that wasn't his original intent?
Or maybe the translation of Episode I's dialogue wasn't perfect. I'm not sure if that should be surprising, since they mistranslated "Leanan Sidhe" as "Rianon Se"... or at least, that's my assumption based on pronunciation and whatnot. But they clearly weren't 100% happy with the translation for Episode I, either. I mean, they even changed Athra to Asura.
I was reading some of the updated database earlier, trying to see if it answered any of these, but it didn't. Although, I did find something interesting about Shion and her glasses. Apparently she has the ability to see into imaginary space...
That is probably why she can see Nephilim, but nobody else. Although, if that's the case, then HELLO CONFUSION I THOUGHT THE OTHER CHARACTERS ACKNOWLEDGED NEPHILIM AT ONE POINT WHEN THEY SHOULDN'T HAVE.
I think it was Jin. Actually, if that's the case, it leads me to believe that Jin also has that ability. Not a plothole/question, but just an interesting observation and sort of a message that means "GO READ THE DATABASE YOU JERKS".
The databse so detailed it even has an article on Albedo and his French puns, plus one about curry. It really would have been nice if they had explained that she wore the glasses to control that ability in the actual game, though.
There are more questions I had, but I can't remember them and I'm tired and hungry and I'm going to bed.
But I swear, there are so many plot holes and inconsistencies with Episode I because of the whole Shion's Subconscious part of the game.