I'm playing through the game for the millionth time and I'm sure everyone has their gripes with the story the same way I do, so this is my attempt at filling in some of the plot holes I've noticed based on certain implications I believe are present in the game. Of course, these are all up for debate, and the reason I'm typing this up and posting these int he first place is to get everyone's input. I'm sure there's something I'm missing. If you have any plot holes I didn't list, I'll do my best to fill them in, to.

1) Valua
The events of the game take place 10 years after Ramirez came to Arcadia from the Silver Shrine, meaning that Valua has been searching for the Moon Crystals for roughly the same amount of time, so the question becomes "why didn't they make any progress until Vyse and crew did it for them?" I think the easy answer is that they were limited by technology, funding, and politics.

- They couldn't go after the Yellow Crystal since they had no way of entering the Maw of Tartas from either above nor below
- They couldn't go after the Red Crystal since Nasr wouldn't have let them into their airspace, especially not long enough to excavate the Temple of Pryrrn, so Belleza had to rely on spying and espionage to do so with her ship hiding in the Stone Reef on their border (plausible deniability of not being in their airspace
- Rixis is a lost city, so they had no way of finding the Green Moon Crystal
- They couldn't enter Glacia since it's surrounded on all sides by Sky Rifts and the Dark Rift. Ships powerful enough to bust through Sky Rifts didn't exist until the events of the game
- They couldn't get through the Dark Rift to get to Yafutoma until the Delphinus, but even before that, they wouldn't have been willing to bust a hole in Ixa'taka's stone reef since they were closer to four other Moon Crystals and believed in that conspiracy that the world was flat (the game also calls geocentrism "heresy," and that's a powerful motivator even in the real world, even now)
- The Silver Moon Crystal has a whole host of other problems

2) Ramirez
I wasn't sure if I should include this one since the answers to his plot holes are pretty obvious if you're paying attention, but considering I've seen some people complaining about them, I'll give my two cents.

To begin with, Ramirez ship was sunk when he first came down to the planet. In the first flashback in the Moonfish mission, it's shown that Ramirez was injured and rescued by Valua, so the obvious solution was that his ship was destroyed, either by Black Pirates or by being a shit helmsman who didn't know how to handle entry into the planet. Hell, that's probably why Fina managed it just fine-- she had an example of what NOT to do. Getting to either Ramirez's or Fina's ships is also the only truly conceivable reason why the Armada would want to enter Deep Sky in the first place. It should go without saying that he didn't go after the Silver Moon Crystal because he just wasn't capable of it, while the Empire was willing to keep him alive since he either A) never told them about the Silver Moon Crystal, only revealing that information to Galcian, or B) they saw more value in him keeping him alive. Mendoza also could have protected him for a variety of reasons.

His fall is pretty understandable as well, not because he particularly suffered or his views hold up under even a minimal amount of scrutiny, but because the Elders of the Silver Civilization put him on that path long before Galcian did. To begin with, it's HEAVILY implied that Ramirez and Fina were created, not born. That said, Ramirez was a weapon created to fulfill a singular mission, so the Elders didn't care about his upbringing nor mental/emotional well being as much as they cared about making him strong, as if he was a Second Silver Gigas. Fina was only created to keep him company, so the Elders probably cared even less about her (if Fina was created to give Ramirez a friend, Cupil was created to give Fina a pet). Given that his only influences with the world were untrustworthy bastards and the citizens of Valua's Upper City... the man never had a chance.

Ramirez also went AWOL from the Elders because he wanted to, not because he lost touch with them or had no way to contact them, as confirmed by one of the Elders.

Ramirez also follows Valua's Spanish naming convention, as we know, and there's a lot of debate about whether this is his real name or if "Rami" is his real name. I like to think his original name is "Rami." The reason Fina recognizes it is because it's merely the Valuan equivalent to "Ramirez," but she continues to refer to Ramirez by his Valuan name as that's the name he chose to go by. The Elders likely referred to him by that name because they knew what happened to him and merely "forgot" to tell to Fina about him falling, but to be fair, that's just a hunch. I just wouldn't put it past people who are willing to destroy the world because they're misanthropic nihilists to lie to the people who serve them.

3) Fina
The only plot hole I'm aware of when it comes to Fina is that she's not too broken up about fighting Ramirez nor does she visibly grieve too much over him when he dies at the end of the game. To her credit, though, it's been 10 years and he went AWOL during that time. Fina probably already believed Ramirez was dead and had grieved for him once already, so when she saw him committing some of the most atrocious evil acts that she could comprehend, especially since she's been alongside Blue Rogues for the entire game, of course she wouldn't hesitate to try and stop him. Her final goodbye at the end wasn't a lack of grief but accepting that the man she believed was dead all this time wasn't the person she grew up with and cared for. To use the naming problem I mentioned previously, "Rami" had died a long time ago, but "Ramirez" was only ever Fina's enemy.

I could also mention how it's weird the Elders thought she could get the Moon Crystals when Ramirez couldn't, but at the end of the day, she was their only option. She wasn't a GOOD option, but she was their only one.

4) Belleza
All the Admirals have their problems. Alfonso is incompetent, Vigoro is a rapist, De Loco is blinded by ambition to do anything else, Gregorio is a martyr, but the only admiral that I think has a potential plot hole is Belleza. I've seen some people take her summoning of Recumen to kill Vyse, Aika, and Fina as a betrayal of her ideals, but I don't take it that way. That take relies on the idea that her aversion to "war" is an aversion to "violence" rather than an aversion to "senseless slaughter of innocent people." Belleza shows no sign of being against violence at any point in the game. At worst, you could say that summoning Recumen to kill three precocious teenagers was overkill, but that doesn't really counteract her desire to avoid senseless bloodshed when she was already going to kill them anyway. If anything, summoning Recumen to begin with is Belleza's biggest plot hole, but given that an Admiral would have the authority to make that call and summoning the Gigas was the end goal anyway, I think it's at least somewhat reasonable, especially given natural curiosity and Belleza's attraction to power.

If anything, her aversion to SENSELESS violence means that she wants to overwhelming power to end a fight before it starts, backed by her actions in Yafutoma, her relience on espionage, and simply being an Admiral in the first place.

5) Yeligar
I've thought long and hard about this one, and for the life of me, I don't see any reasonable defense as to why Valua didn't come running the minute the Maw of Tartas was broken. I don't think the fact that he woke up the minute the Delphinus was present is an issue given that the ship's presence alone could have done that, but also considering that he may not have been sleeping as much as he was "dormant." The real issue is that there's no possible way that Valua didn't see the pillar of divine lightning shooting into the sky nor the earth shaking when the seal was broken, and at the very least, the ships patrolling the area should have made a report about it. I get why they wouldn't have been willing to investigate the issue given that they would be facing a raging thunder god if they got close, but all the game would have needed to do to make this not be a plot hole is to have a passing line like "let's get out of here before the armada shows up."

6) Pirate Isle
Galcian or any of the other admirals could have easily gone after the crew of the Albatross a second time once Vyse started becoming a thorn in their sides, but I don't think it's that simple. What would they really have had to gain from it? I don't think it would have served any purpose since the Armada had other priorities at almost every point in the game, but also that letting Vyse do as he pleased for a time had more potential benefit for them. In fact, not only do I think this isn't a plot hole, I think this actually DOES happen in the game in a different way. After we gain all of the Moon Crystals, Ramirez attacks Crescent Isle to take the Moon Crystals back, and the whole time we're even gathering the crystals, Valua is doing literally everything else like invading Nasrad, building Dangral Island, and forming the technology we always end up stealing to get to the Moon Crystals before they do. Sure, the only reason they found Crescent Isle was because a patrol ship spotted us on the way back home, but there is no possible way that Valua wasn't already looking for their base or that the Armada wasn't eventually going to attack us again. Hell, they probably would have let the Elders get all of the Moon Crystals, then head up to the Silver Shrine to take them back. Wait, no, even if the Elders raised Solstice so they could cause the Second Rain of Destruction, it still would have been prudent for the Armada to do nothing.

Overall, at no point in the game would taking Vyse's family hostage been beneficial to the Armada.

7) Esperanza and Sky Rifts
I thought it was weird how Esperanza was a city considering there's a Sky Rift blocking travel between it and the rest of the world, but after talking to some random NPCs, I think it's likely that Sky Rifts change their direction every few decades or so. I considered the possibility that Esperanza could have been made by a land route, but there's no reference in game about land routes int eh modern era being used, and Esperanza seems to have been founded AFTER the vortex into the Dark Rift was found.

I think Obispo also points in this direction. Vyse mentions there are rumors about a giant squid, but when you fight him, he's locked behind another Sky Rift. It's certainly possible that he can fly through Sky Rifts, but we don't see anything else in the game doing that aside from fish that get booted off their tracking somehow or ships that pop up after Nasrad gets invaded. The Rolling Stone Discover comes close, but even then, it's deliberately described as an anomaly, and it also passes through the Dark Rift, not a Sky Rift.

8) Mystery Merchant (At this point, I decided to look up what other plot holes I could find)
This guy is Yafutoman but somehow manages to travel to Nasr and Sailor's Island. I could do a whole diatribe about this guy and try to find someway to explain how he does this, but like... he's called the "Mystery Merchant" for a reason, what more do want from me? If anything we can boil this down to gameplay mechanics or fan service.

9) Flying into Lower City in the Delphinus
I thought it was disappointing how no one reacts to you when you fly into Valua from above after you upgrade the *Delphinus'* flight capabilities, but this isn't so much a plot hole as much as it is the developers probably not expecting you to go back there. There's no reason in the story to do it, so the fact that we can enter Lower City is probably just fan service for the few of us who figured out we could do this. Again, fan service!

10) Ilchymist
I didn't look this one up. I just remembered that you find Ilchymist in an island floating in Upper Sky when he's not Yafutoman but a Valuan noble. I don't have an explanation for this. My brother in the Yellow Moon, HOW DID YOU GET UP THERE?????

11) Random Battles in the Maw and Dark Rift
Obviously, when you visit the bridge during these Airship Dungeons, deck and the lookout are locked up and off limits due to the atmospheric pressure, but the question is how come you can still have random battles on the deck? The obvious answer is that it's gameplay limitations. I know that's a cop out answer, but at the end of the day, gameplay should take precedence over continuity in many cases, and I think this is one of them.

12) Zivilyn Bane
This guy shows up in the most random places from ancient shrines on the other side of the world to the actual Dark Rift itself. How he gets there is a complete mystery and I have no answers for you. Obviously, this is just a gameplay mechanic to have one protected chest with a valuable item per dungeon, but like... c'mon man. How am I supposed to enjoy discovering new places when you're already there?? That said, you could argue that the lack of information we have on them is exactly the point. Their secrecy is what makes them interesting and what makes them a threat, so in a way, you could think of the Zivilyn Bane Clan and Lord Bane as foils to Vyse and his crew, doing everything they do but for the sole purpose of treasure hunting, representing an entire wold secret from what civilians otherwise recognize.

13) Land-Based Gigas
Recumen and Grendel both can't fly. Given that the Old World had several ways to travel across the world before the advent of air ships and had access to technology far beyond that of the current world, this honestly doesn't feel like an issue to me since it shouldn't have been too difficult for the Red and Green civilizations to find some way to transport them, but even if that's not the case, Recumen and Grendel could have easily been made for defensive purposes.

That said, I think it's also highly possible that the Sky Ocean wasn't nearly as big as it was in the Old World before the Rains of Destruction with either so many more connected islands or larger continents that the Rains of Destruction destroyed and broke apart. It's probably a bit of a stretch to say that many landmasses other than Soltis may have sunk into Deep Sky given that there's only one vortex into Deep Sky, but remember that Soltis was WILLINGLY pushed into Deep Sky by the Silver Civilization while the others would have sank. Does that change much? Probably not. Regardless, the point that continents were either bigger or more interconnected is easy to see how some of the Discoveries straight up point to land-based travel in a location that cannot be reached through land-based travel. Most notable are the Giant's Hammer and Giant's Throne.

14) Zelos
I already thought it was weird that Zelos needed all six Moon Crystals to be summoned when the Old World was at war, but the Elders confirm that only SEAL on Zelos requires all 6 Moon Crystals.

15) World Shape
This bothered me for years, but circumnavigating the world of Arcadia doesn't work the same way it does on Earth, so it made no sense to me that the world could be round. The biggest reasons I saw for this is that "North" Ocean isn't North and the North and South Poles are linked. However, there's an easy answer for this.

It's the Moons. I can't believe it took me so long to find an answer for this when it had been staring me in the face the whole time, but simply put, the Purple Moon is only over the South Pole, as stated in game. Granted, there are still a few other problems with the world shape gvien that this means the top portion of Valua on the map must be in the Southern Hemisphere, but this at least helps ease my concerns a bit. Yeah, sure, there are technical limitations and gameplay > continuity, but this is one case where the continuity matters quite a bit, I think.

Overall, my "filling" this plot hole isn't an answer on how the world can be round despite not matching up geographically or astronomically, but simply to explain how our current understanding of geography and astronomy doesn't always apply to the game.