- Mewtwo. While Pokémon who are abused usually grow afraid or mistrustful towards humans, this one was driven half insane by him and decides to use its extremely powerful psychic abilities to exact his revenge, human and Pokémon alike. Given his game counterpart's ability in the later series to take on, and possibly even beat, other Legendaries, including Arceus, the god of all Pokémon itself, it's a very good thing for the universe in the anime that Mewtwo eventually decides to take a more productive approach to finding his purpose in life. The last thing Ash and his friends need is a Pokémon version of Kratos or Sephiroth running amok.
- Mewtwo's "Uh-Oh" Eyes deserve a mentioning all their own. Between having Glowing Eyes of Doom, Hypnotic Eyes, Hellish Pupils, and an unwavering Kubrick Stare, this guy has one terrifying gaze.
- The fact that he doesn't realise that his creator is dead may be weird for some viewers.
- That or Mewtwo may not even care. Not that he would have any reason to—although the one-shot manga took it a step further in that it killed Fuji, its father-figure, on request to take his knowledge of Mewtwo's creation to the grave. It's implied Mewtwo has nightmares about it.
- Mew himself, despite all his cute antics, turns out to not be as nice nor harmless as it first appears, as after Mewtwo attacks him and sends him flying into the sky, Mew retaliates with equal force, blasting Mewtwo right through a wall. From then on, they engage in a titanic psychic battle, with Mew striking with entirely merciless and lethal intent. In the Japanese script it also appears to have a low opinion of the clones compared to the originals.
- This promotional photo.◊ Notable in that it depicts Mewtwo in Evil Overlooker fashion... with its mouth open, despite the fact that it never does so in the actual movie. Which, to be honest, makes the image all the creepier.
- Slightly Nightmare Retardant as they forgot to draw Pikachu's mouth, though.
- In the Japanese CD drama, The Birth of Mewtwo, one scene involves a fight between Giovanni and a random trainer. After Mewtwo defeats the trainer's Magmar, it steals the poor Pokémon, then orders Mewtwo to attack the child.
- Earlier in the same CD drama, when Mewtwo's starting to go berserk, the computer shoots him dead. Yes, it was confirmed dead when the monitor flatlined. Mewtwo got better using Recover, of course, but that and the talk of Mew being immortal still adds Fridge Horror that more-or-less confirms Mewtwo literally can't be killed.
- Mewtwos creepily organic cloning machine. The robotic hands that grab Ash are articulated like human arm bones, and the clones, when born, get pushed out from their tubes with a nasty squishing noise.
- The "evil" black Poké Balls sent to capture every trainer's Pokemon. No matter what they do, they just keep coming back. Poor Pikachu in particular was practically fighting for his life trying to outrun them.
- For double the nightmares, keep in mind that later episodes of the anime make it impossible to catch another trainer's Pokémon. Mewtwo basically just used something that's capable of breaking the rules. And for triple, imagine the balls used as being the same type Giovanni must have used to capture the Magmar as stated above. For all intents and purposes, Mewtwo must have used Giovanni's own tools against humanity.
- The entirety of New Island, where Mewtwo resides, looks like something out of the mind of H.R. Giger.
- When Team Rocket stumble onto Mewtwo's cloning laboratory, two moments in particular stand out.
- First, when the computer detects a viable Pokemon DNA sample, that being Meowth, and attempts to put him in the cloning machine. It starts out a little funny with him complaining about it, until he actually goes into the machine, where James grabs him to pull him out, and Meowth is begging for help, literally crying from sheer terror. Jessie and James barely manage to pull Meowth out, but the machine still manages to pluck a few tufts of fur from his tail. It then uses those hairs to complete the cloning sequence, and Meowth's clone slides down the cloning tube. The trio is severely creeped out by the result.
- Second, the music that plays immediately after , as the machine reads Meowth's DNA sample. The first 15 seconds are creepy enough to put anyone on edge, giving the cloning a sinister, unnerving vibe
- Nurse Joy as Mewtwo's servant; her mindless, almost robotic movements and expressions firmly cement her in the Uncanny Valley.
- Even worse, there are a few moments wherein she and Mewtwo speak in unison with each other—the effect makes it sound as though he's speaking through her, complete with their voices melding together. It makes her seem less like a brainwashed robot and more like a puppet.
- Ash's petrification, where he isn't just blown away by Mewtwo and Mew's combined blasts of energy, but instead turned to stone.
- The big battle between the natural Pokémon and the clones. We've seen Pokémon fight before, but the obvious lethal intent and the sheer brutality made the whole event absolutely horrifying.Nurse Joy: Pokémon aren't meant to fight. Not like this. What can come out of it?
Neesha: Nothing but pain...
Nightmare Fuel / Pokémon: The First Movie