** Rourke's willingness to condemn the Atlanteans to death despite Milo's protests.
** That whole scene where Milo does away with [[spoiler:Rourke. Milo stabs him with some broken glass from Kida's containment box and turns the man into a roaring, demonic crystal creature with red eyes]]. The creators of ''SilentHill'' would be impressed.
** Even before that, when [[spoiler:Rourke]] is trying to kill [[spoiler:Milo on the zeppelin]]. Before, hey, he's a little angry HOLY SHIT [[AxCrazy HE'S GOT A FIRE AXE]]!!!
** The fact that [[spoiler:''he was still going after Milo even after being transformed?'']]
** Or when Rourke [[spoiler:throws Helga from the balloon and she falls between the propeller blades? Not to mention the implication that the fall broke her back.]]
** How about the [[SlasherSmile smile]] he has after he gets the ax?
** Not only that, but look at his [[spoiler: crystal form]]. Kida's is glowing and almost angelic. [[spoiler: Rourke's crystal form looks like it came from the depths of Hell]].
** His scream when he [[spoiler: goes crystal]]. Jesus!
** [[spoiler: Rourke's]] transformation in general.
* The Leviathan. It's a crustacean-shaped MagiTech MechanicalMonster with [[GlowingEyesOfDoom glowing]] [[RedEyesTakeWarning red eyes]] and a deadly particle beam WaveMotionGun. Given that the sphere in the front of the Ulysses has at least seven visible decks, each with a decent amount of headroom, the entire ship winds up being around a thousand feet long. The Leviathan's larger claws are large enough to wrap fully around the Ulysses, and from turn-arounds, appear to be somewhere near a twelfth of the Leviathan's total length. That gives the Leviathan a length that would be better measured in miles (being somewhere in the range of 12-14 thousand feet long, or 2-2.5 miles).
-->'''Rourke''': What is that, a pod of whales?
-->'''Mrs. Packard''': Nuh-uh, ''bigger''.
** One has to wonder... ''what the devil was it built to defend Atlantis against?!'' The other cultures of Earth were at the dugout canoe stage, at best! (The sequel provides at least one candidate in the form of the Kraken...)
*** Atlantis IS an Empire, and the King was trying to wage war (against Athens, judging from Plato's texts...). Which also creates another point of nightmare fuel: imagine you are one of those people in a dugout canoe, just minding your own business... when suddenly a two mile-long LOBSTER OF DEATH erupts from the water, flies over to your village (it was flying in the prologue) and flash-fries it in an instant.
*** Worse, the opening shot of the Prologue shows that there were four of them coming in formation from a single direction. Atlantis had a FLEET of those monstrosities.
* The Crystal Chamber can be considered Nightmare Fuel, if only in the sense that it's an eerie environment. Think about it: It's underneath the city, in a darkly lit cave, where the only light source is the Heart of Atlantis, which gives off a creepy, blue glow. Not to mention that, hovering around the Heart, are huge, ominous rocks carved to resemble the faces of ancient Atlantean Kings. To a child watching the movie for the first time, it can be somewhat unsettling.
** What's more unsettling to me is the part where Kida [[spoiler: transforms into the crystal being]], because anyone can tell that that's not really her anymore, just some...thing [[PeoplePuppets using her body as a vessel]].
--> "'''''[[VoiceOfTheLegion SOH-lesh MAH-toh-noat MY-loh THATCH-toap. Kwahm TEH-red-seh-nen.]]'''''" [[note]]"All will be well, Milo Thatch. Be not afraid."[[/note]]
** When the Heart senses Rourke's presence, its color goes from ethereal blue to ''blood red''. And the mysterious humming noise it emanates? Closed captions describe it as ''murmuring voices''.
* The opening scene of the movie provides some FridgeHorror. After an introductory quote from Plato, we're treated to a scene of a calm ocean landscape. Suddenly there's a bright flash and a fleet of Atlantean vehicles outrunning ''a mushroom cloud.'' The king later explains he wanted to weaponize the crystal, apparently as an ancient equivalent to an '''''atomic bomb.'''''
** The sinking itself is also chock full of this. Nevermind Kida losing her mother, the barrier doesn't cover the entire city, leaving those trapped outside to die.
* From the sequel. The [[EldritchAbomination Kraken]] is so large we never see the entire thing in view. Only closeups of its body...
** Actually, you do see the whole thing at one point. Doesn't make it any less horrifying.
** Not only that, but it can also hypnotize you.
** There's a deleted scene where a woman is asking her baby to give her a hug and [[spoiler:it's a baby Kraken]]. *shudders*
** Edgar Volgud, the antagonist of the Kraken arc. He essentially [[DealWithTheDevil made a deal with the beast]] and took away the spirit of the Norwegian town where the Kraken resides.
* Also from the sequel. The Dust Coyotes. Imagine you are just walking along somewhere, not a care in the world and suddenly a dust storm appears out of nowhere. Then you hear the howling and thousands of [[RedEyesTakeWarning red eyes]] start staring at you with possibly malicious intent. Then the dust takes on the form of thousand coyotes, all of which are snarling and howling and probably with the intention of ripping you to shreds. Imagine seeing them at night. Yeah, [[SarcasmMode sweet dreams]].
** And if that wasn't enough, the villain of that particular part has...''something'' done to him by these coyotes.
* Surtr, a giant fiery demon summoned so that Ragnarok may begin... [[NearVillainVictory AND HE ALMOST SUCCEEDS]].
* Ymir. He's so big he's [[ThatsNoMoon mistaken for a mountain]].