* When you break into [[spoiler:the Biorite facility]], you come across a room containing about twenty save crystals. Nothing special about them, there's just a lot. [[BigLippedAlligatorMoment Nobody mentions anything about it.]] But if you [[BonusDungeon return to]] [[spoiler:the Third Entalar seal]], you'll encounter "Killer Crystals" that try to eat you. That room was housing the experiments that created them!
* The Gate To Elysium and the Four Towers (see WMG) have no explanation about how they exist, appeared, were created... But when you discover what [[spoiler: [[TheLifestream Biorite]]]] truly is (and the ultimate secret boss), then you realize it's been made by [[spoiler:''the planet itself'']], in a form of purgatory.
* [[IdiotHero Hilbert]] literally has a low intelligence stat.
** And Ethan, whose life has basically been one long string of bad things happening to him, literally has a low ''luck'' stat.
* In TheVeryDefinitelyFinalDungeon, you encounter a GiantSpaceFleaFromNowhere MiniBoss named "Pollux". At first, it just seems weird and random, but then you realize that [[spoiler:the BigBad is named "Castor". Castor and Pollux were the twins that were turned into the constellation Gemini in Myth/GreekMythology.]]
* Castor gains a few more AntiVillain points when you realize that he probably had no idea that [[spoiler:Ethan was awake the whole time he was buried in biorite. According to what Barasur said about [[GoMadFromTheIsolation Tiamat]], she was conscious because she was sealed against her will; all the other Havali were sleeping normally because they didn't fight it. Helio said he didn't tell Castor [[MoralEventHorizon everything that went on at the facility]] and no one knew about Tiamat at that point, so Castor likely didn't realize that he would be putting his little brother in an AndIMustScream state]].
* Three major forces are called the Republic, the Empire, and the Kingdom - so you won't mess up even if you can't remember any names.