* 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: 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, ie. ''reality incarnate''. There's no way guys like them would fall to those simple {{Mooks}}]].
* 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.]]