The Team Rocket grunts walking towards Lance in a thuggish and weird manner can be either unintentionally funny or creepy.
The way Agatha's Gengar comes out of its pokeball in "The Challenger" is a healthy dose of both this and Awesome.
The Legendary Beasts perishing in a burning building in The Reawakening. The fact that we only see it in silhouette makes it both better and worse at the same time.
In Courtney's vision, Primal Groudon awakening and sending out a gigantic fiery laser beam over several Hoenn islands, completely destroying them. Then it turns on Maxie and crew...
Courtney herself is just as psychotic-yet-childlike as she was in ORAS, but it's somehow even creepier due to being fully voice acted and animated. Especially with how her voice goes from unsettling, soft monotone to borderline orgasmic in her last few lines, and her creepy giggling right after it, at the mere idea of "engaging" and "analyzing" Brendan, a roughly twelve year old boy.
Primal Kyogre's rampage is nothing short of an apocalypse, complete with Ominous Latin Chanting. Upon awakening, the weather goes completely berserk, with heavy rain, intense winds, massive maelstroms, thunderstorms, and tornadoes appearing everywhere. Hundreds of Pokémon, whether they be on land, in the air, or under the sea, are trying to flee from the chaos with absolute terror on their faces. The short ends with Primal Kyogre about to devour Team Aqua's ship.
Primal Kyogre shows us how utterly terrifying Legendary Pokémon are - more than just living beings, they're primordial forces of nature. In less than a minute after being broken out, it has completely warped the weather into the unholy trinity of Perpetual Storm, Mega Maelstrom, and Dramatic Thunder - and everything is suffering as a result while Primal Kyogre itself is levitating in the middle of a trio of typhoons.
The one moment which informs you that Archie has fucked up: Primal Kyogre's Eye Awaken. Sleep tight.
Let's forget about the storm itself for a moment and take a look at those maelstroms. We get treated to a shot of Mossdeep City's island, which has multiple cities on it, surrounded by maelstroms. If you look closely, you'll see that the maelstroms are larger than the cities.
How about the fact that the currents are so absurd that not even deep sea Pokemon are safe from harm, showing that even Water Pokémon are threatened by Kyogre. Likewise, this shows that Kyogre's Drizzle/Primordial Seas are far, far more than the endless torrential rain that most tend to think, compared to Groudon's mini-sun-induced drought (re: burning sky).
Even scarier is the difference in demeanor of the two. Primal Groudon's "Desolate Land" does not have as drastic an immediate result as Primal Kyogre (possibly not triggered yet), but it immediately fires off one Solar Beam at a group of islands and blows them apart, and another at Maxie's group almost as an after-thought. When Primal Kyogre awakens and breaks the surface, it immediately kicks off a cataclysmic storm, but that is not the worst part. When Archie futilely pleads for Kyogre to listen to him, its pupils immediately dilate in mad anger, and it makes a beeline straight for him. In other words, solid evidence that Primal Kyogre and Groudon are driven mad by their immense power, if Kyogre reacted as such to Archie calling him out.
Deoxys' transformation from that triangle to it's usual appearance is full of Body Horror.
Deoxys immediately makes the connection between Rayquaza and Brendan/May and goes to attack the kid when they're standing on the satellite, slicing into the wing of the satellite they're standing on.
The Old Chateau is much, much creepier than in the game. Some of the stuff going about is more reminiscent of Electric Tale's Black Fog than a regular ghost-type.
One of the creepiest things about this episode is how it uses Nothing Is Scarier, especially at first. There are long periods where nobody says or makes the slightest sound save for footsteps. It really shouldn't be creepy, but it somehow manages to be scarier than it would be if ghosts were all over the place.
During the dinner scene, Chansey and Cheryl look down at their empty plates and act as if they're seeing and tasting food. There's a long silence as the camera repeatedly zooms in on the empty plates as the cutlery keeps grinding against the plate. The thing that makes it creepy is the fact that the animation is clearly done as if they were eating food, but they could have just been hallucinating it while the audience sees that they were clearly eating nothing.
While they're "eating" the ghostly butler is watching with a creepily happy look on his face, as though he's waiting for something. Once Cheryl takes her last "bite" (and while she's doing so she looks dead-eyed), he gives her a look that screams "gotcha!" And we never find out why he's reacting this way...
The realistic design works for it. If it wasn't for Chansey or Haunter, anyone could have thought that they were watching another anime rather than Pokémon. And then there's the ghost girl from the end of the episode. While the anime had its few creepy moments (e.g. Sabrina and her living doll), it pales in comparison with the ghost girl. She is like an animated version of a Stringy-Haired Ghost Girl straight from Ringu or Ju-on that pulls out a Nightmare Face. What Do You Mean, It's Not for Kids? indeed.
Though it might be unintentional, the close-ups of Chansey's face were generally viewed as really creepy due to how Chansey was depicted in the show's art style.
Episode 11, "The New World," features Team Galactic, showing off Giratina in all of its eldritch glory. When it is summoned, it appears as nothing but a huge shadow, and, after freeing Dialga and Palkia, dives into Cyrus, and when Giratina has disappeared, Cyrus has too. All the while Cyrus simply stands by, staring at it unflinchingly. Eventually, Cyrus wakes up to see Giratina looming over him, and he finds out that it took him to the Distortion World, which is already eerie enough as it is. But the creepiest thing is how content he is in staying in this world of nothingness, and how coldly he says for the rest of Team Galactic (who are all currently in a panic, wondering where their leader went) not to look for him, while Giratina fiercely roars in the background as if also telling them to not look for Cyrus, who is now its only companion.
Even when in the Distortion World (and thus no longer an amorphous blob of shadow) Giratina remains incredibly creepy. While Cyrus ponders the nature of the Distortion world, Giratina just unwaveringly looms over him. And stares.Cyrus doesn't seem to mind, though, which either makes this silly or worse, seeing as he just doesn't care...
Giratina's appearance in the "regular" world is... different. Remember Giratina's appearance◊ when emerging in Platinum? Not being limited to the DS's hardware has let Game Freak recreate it into this...◊ thing - this melting, shadowy, sludgy thing.
Adaptations of the Sinnoh games vary on how they portray the Red Chain's control. Here, Dialga and Palkia are covered all over in restrictive and painful-looking chains. And when Cyrus issues commands, these chains dig into them. It's little wonder why they both fled when given the chance.
Episode 14, The Frozen World, features Team Plasma in their Black 2 and White 2 incarnation, and their attack on Opelucid City. The Plasma Frigate launches what is basically an ice nuke, a laser fired at the city that makes the air a lot colder. You can see the buildings starting to frost over. Then Colress amps up the power and the entire city is frozen solid, just like in the games. It's definitely depicted as a Weapon of Mass Destruction, and there's no telling how many lives were lost during this attack. Because unlike the games, where you don't really see too many people, you actually see a lot of people in the city panicking and trying to flee from this very real danger, and towards the end you see many of these people standing still on the streets, frozen alive.
Before the Plasma Frigate enters the scene, the episode opens with the peaceful skyline of Opelucid suddenly ripped apart by several explosions caused by the attacks of Team Plasma's Liepards, which are shown to explicitly target buildings. People panic and flee, some of them tripping and falling on the way. You are watching a terrorist attack unfold.
Episode 17 features something rather graphic in tone. Essentia's Espurr, Mimi, walks up to her and rubs against her leg affectionately, knowing that this mysterious figure is actually her owner, Emma. Essentia's response? She slowly puts her foot back, and KICKS MIMI. Granted, this is something that's happened a few times in the anime, where it's usually Played for Laughs. But that isn't the case here.
Cyrus doesn't seem to mind, though, which either makes this silly or worse, seeing as he just doesn't care...
