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When you blow up Andross' face in Star Fox 64, it turns into one of two things: a robot head (on easy route, see above) or a giant brain (on hard route). Both are terrifying.
A Huge Holographic Head floating in space is pretty much routine in Starfox, but the one in the very first one may rank as the creepiest due to the untextured polygons and basic early 90s geometry combining for an Uncanny Valley effect. In addition, when taking the hardest path to this fight it will grow horns as a Cosmetic Award.
The RedEyes in Star Fox Adventures. Words cannot describe the brix that were shat by the players when they stepped out of the Arwing for the first time and saw freaking enormous T-Rexes roaming everywhere! And for half the level you can't even kill them! And don't even mention the RedEye King.
Also in Adventures, Dragon Rock. The music and visuals alone are very unsettling, and then there's the imprisonment of dinosaurs, the enemies within, and the boss Drakor.
Out Of This Dimension from the original. Mind Screw doesn't even begin to cover this... The intro to that level is Pepper trying and failing to reach Fox and co. as if they just disappeared. And then at the end of the level, the words THE END pop up in front of Fox, who's just stuck there. Until the player dies. You literally get trapped in another dimension with no way out and Corneria is doomed. This level may very well be a Downer Ending or a Non-Standard Game Over.
The horrible grin of the "laughing meteor" from the SNES original: ◊ — the thought of a giant, evil looking grinning THING floating in space is extremely unnerving for some.
The Aparoids. They are able to possess not only machines, but organic life forms as well. It doesn't help that their victims are still awareof what they are doing. They start out pretty tame: they're brightly colored and have a few funny-looking forms. Then in the later levels we see them assimilating everything. More and more they resemble techno-organic hybrids that just seem disturbing. Then there's what happens to Pigma... not a well-liked character, but holy crap, that is not a pleasant fate. And what he becomes has the following exchange in a deep, almost demonic voice:
Fox: Looks like he's already gone... who or what are you!?
Aparoid: We will answer. We are the ultimate existence. You cannot resist us. You will join us.
Then there's the Aparoid Queen. She speaks in the voices of the deceased or assimilated... including James McCloud. The psychological horror she's inflicting on the heroes by this is evident in their reactions. And the only coherent thing she says in her true voice?
Queen: All for us. Everything in the universe exists for us! Bow before us! SUBMIT TO US!
Seeing Corneria City almost entirely ruined is either this or depressing as heck.
Aquas from 64. The level quickly gets very dark (you can use your unlimited torpedoes to brighten things up slightly, but it doesn't always help), with endless quantities of hostile sealife appearing out to the gloom to attack you. Even the boss of the level, a giant clam, manages to be pretty scary when you first approach it and can't quite make out whether or not it's actually an enormous mouth.
That's even without the depressing/horrific backstory of the planet mentioned in the official strategy guide: The boss of this level, who existed long before Andross, commanded thousands of the starfish enemies to the planet's polar caps and had them explode, instantly melting the polar caps and flooding the entire planet, killing all non-aquatic life.
As seen on the main page for the original game, the Star Fox team is depicted looking like realistic animals in artwork. Needless to say, they look incredibly freaky. Thank goodness Nintendo stuck with the cartoony look in-game afterwards.