* The Nopon terms for High Entia and Telethia ("bird-people" and "dino-beast," respectively) are surprisingly meaningful once you discover [[spoiler: how the two are related. After all, didn't birds evolve from certain species of dinosaurs?]]
* After TheReveal, it makes a lot more sense why The Monado can't hurt Faced Mechon. [[spoiler: The Monado can't hurt Homs, and Faced Mechon [[WasOnceAMan ARE Homs.]]]]
** [[spoiler: There is even a conversation with Linada that says that the red lines on Faced Mechon are tubes pumping the Homs' blood though it.]]
* [[spoiler: Shulk's HeroicRROD on the way to the Mechonis Core happens not long after he tries to make the case to Egil that Mechonis and Bionis can live in peace. I guess Zanza really didn't appreciate Shulk going OffTheRails of his grand plot to destroy Mechonis.]]
** [[spoiler: Also note that the Apocrypha Generator was still active at the time. It's possible that Zanza was trying to ''kill and/or possess'' Shulk at that point, like he did with the Monado's previous wielders, and it was only because the Monado's power was suppressed that Shulk survived more-or-less intact.]]
* {{Guest Star Party Member}}s Dickson and Alvis are effectively unbeatable when they fight alongside you, their HP never droping below one. That's kind of silly [[spoiler:until you figure out their true identities. Dickson is Zanza's disciple, granted with immortality; and Alvis is Monado, i.e., ''reality incarnate''. There's no way guys like them would fall to those simple {{Mooks}}]].
** Likewise, [[spoiler: the HopelessBossFight with Zanza also has Fiora equipped with the Unbeatable IV gem, like the 2 above. She has Meyneth inside her body, who's a God herself, and could stand toe-to-toe with Zanza.]]
* While there is a canon explanation (that is AllThereInTheManual) for [[spoiler:Fiora getting her old Homs body back (there's a machine that can regenerate her body, that they used after her upgraded abilities were no longer needed)]], there's a plenty plausible reason for it even without that. At the end of the game, however briefly, [[spoiler:Shulk is basically god.]] If there was one thing he'd want to do with that power, wouldn't [[spoiler:giving Fiora her body back]] be right on the top of the list?
* A minor one, but the icons for Landmarks on the map are [[Creator/MonolithSoft monoliths.]]
* Early in the game, it is established that falling debris is a common problem for Colony 9. Then, after one debris alarm, this is never brought up again. It occurred to me that there was a very good reason for this - On Bionis' leg is Colony 6, which had frequent altercations with Mechon. The one time the debris alarm is brought up is the day before the Mechon attack on Colony 9, when the Mechon assault on Colony 6 was drawing to a close. The debris that keeps falling into Colony 9 airspace? Wreckage from the battle, both Mechon and Homs machinery alike. The reason it stops? Because the battle for Colony 6 came to a close.
* During the cutscene that take place in [[spoiler:outer space]] shortly after [[spoiler:Zanza emerges from Shulk's body]], you can see [[spoiler:numerous features of our own solar system, such as planets and asteroids.]] The presence of these things makes a lot more sense after you learn that [[spoiler:the universe of Bionis and Mechonis was created right after the old universe (the one in which we live) was destroyed, so the features in our solar system, just like Shulk's mortal consciousness, were never supposed to belong in the new universe in the first place.]]
** [[spoiler: The places where the two important races in Xenoblade- Machina and Homs- were created from on the Bionis and Mechonis reflect their hosts opinions of them.]] The Homs come from the feet of the Bionis, [[spoiler: representing how Zanza feels little for them, like they should grovel at his feet]] while the Mechon [[spoiler: and Machina come from the Mechonis's chest, representing how Meyneth loved them (seeing how the heart is usually located in your chest, and that's said to be the "love" organ).]]
* Why does White Eduardo only show up during thunderstorms? Albinos tend to sunburn pretty easily, and Brogs are (seemingly) amphibians at that.
* Gem crafting reveals that as a shooter, Riki's the best at making Gentle flames while the worst at everything else. Actually using him for gem crafting reveals that Riki uses his normal arms instead of his wings in order to fiddle with the gem furnace. Riki can't reach the valves in order to make the flames any hotter due to him being the shortest playable character in the game.
* One may be wondering why someone as old as a Nopon Sage would have the voice of a Nopon child. While his age can be excused by the fact that he's seemingly magical, defeating the Unreliable Rezno, a mythical monster only previously beaten by the Nopon Sage himself, reveals that the monster is apparently the source of the Ocean Elixir of Life. In other words, the Nopon Sage, himself, had subjugated into a permanent FountainOfYouth in order to survive as long as he does today, with the side effect of regressing back into the form of a child.
* The track "You Will Know Our Names" usually plays against Unique Monsters, but it also plays during two storyline boss fights (instead of the usual "One Who Gets In Our Way"), against Metal Face and against [[spoiler:Dickson]], both on [[spoiler:Prison Island]] at that. And incidentally, [[spoiler:both of them are Dunban's former war comrades turned traitors]]. You will know their names indeed.
* Egil's Gold Face Mechon is named Yaldabaoth. This seems like a random name until you progress further into the story. Yaldabaoth in Gnostic mythology is an arrogant solar deity who suffers from a complex of cosmic egotism and falsely believes himself to be the only god in the entire cosmos. [[spoiler: Sounds like a certain Zanza that Egil wishes to destroy. In naming his Mechon Yaldabaoth, Egil mocked the fuck out of Zanza to boot]]. Also worth pointing out is that Gold Face has a tail; while unusual, it represents the Gnostic Yaldabaoth, who is a serpent.
* It seems unlikely that no person ever discovered the fact that [[spoiler:High Entia spontaneously mutate into Telethia when exposed to large amounts of ether]]. For one, it seems to be very easy to just [[spoiler:accidentally turn into one]] if that were the case. However, given that there are still Telethia flying around Bionis [[spoiler:without Zanza's presence]] indicates the possibility that [[spoiler:some DID turn into Telethia and the ones still remaining are just mutated High Entia]]. After all, it is implied that previous High Entia rulers did know about this and tried to keep it a secret.
* One of Shulk's first [[CombatClairvoyance visions]] shows the Arachno Queen ''impaling and killing Reyn in one blow.'' If it weren't for Monado Shield [[DieOrFly kicking in just in time]], [[spoiler: Shulk would have lost ''both'' of his best friends within days of one another.]]
* Shulk's visions of the future in general. It might seem awesome at first to be able to predict something is going to happen and thus stop it, [[BlessedWithSuck but the downside is he has to watch his friends and loved ones be brutally slaughtered over and over again.]] Of note is [[spoiler:Fiora's supposed death,]] which Shulk gets his warning but is powerless to actually do anything about it, which means he has to watch her die twice.
** Three times, if you count the vision he gets when putting the Monado back before the attack.