By all accounts, this is simply a super-hard mode of Pokemon Crystal, so you would only expect nightmare fuel from Pokemon Crystal. However, with numerous changes, there are also some unsettling aspects that wasn't present in the original...
- The idea that Team Rocket becoming a competent criminal organization made real. Every Rocket member possessing a rare and usually very strong Pokemon, ambushing the stairs, ensures that you don't feel safe. And the fact that Team Rocket gets so strong that they are higher leveled than seven gym leaders...
- The Team Rocket Mahogany Hideout already was creepy in the original, with a very unsettling track, and a pretty ominous atmosphere. But Crystal Kaizo managed to ramp up the scariness factor, with the fact that the hideout is almost pitch black on the first basement, unless you use Flash... and then the hideout becomes dimly lit, and almost every step you take, you trigger a trap that reveals a dangerous Electrode or worse...
- The Goldenrod takeover becomes this in Crystal Kaizo. In the original, Team Rocket were only blocking random, out of the way areas. But in this game? They were blocking the city's entrance and exit, completely locking down the city, and preventing anyone from entering or exiting. The only way to get inside Goldenrod during the takeover is by flying. And two of them are blocking the way into the Goldenrod Dept. Store, trapping numerous people inside, and preventing anyone from purchasing healing items... And Team Rocket almost completely blocked the way into the underground, the only way that leads to the underground warehouse. If not for very tiny gaps of water, and a very small gap in their security, they could've easily completed their plans. It goes to show how they mean business.
- Some of the Rocket members' Pokemon can qualify, considering the methods of obtaining these Pokemon.
- There are fossil Pokemon and the Porygon family, which can only be obtained by resurrecting them, while the other is a man-made Pokemon. And one of their careers is finding fossils and reviving them. The scientist with the Omastar states that he doesn't care if Pokemon are hurt by their experiments.
- A couple of Team Rocket members have a Gyarados on their teams. While they might be tamer than most Pokemon in-game, considering the Lake of Rage scheme and the fact that Gyarados are huge and vicious Pokemon capable of destroying cities, are now in the hands of rocket grunts.
- A disturbing number of them have Pokemon that knows Explosion, meaning they will willingly sacrifice their own Pokemon to take down their enemies. Who knows what else they could do with that.
- Two Team Rocket Members have a Slowbro and a Slowking, which is used by the leader. And a Slowpoke Tail is found near the grunt with the Slowbro, guarding the password "Slowpoketail." Right after undergoing an operation with cutting off the tails of slowpokes in the well, some apparently didn't escape the tortures...
- Some happiness evolution exclusive Pokemon like Espeon, Umbreon, Crobat, and Blissey, are sometimes found on team rocket members teams, which may seem unusual considering that they don't seem to care about the Pokemon that they exploit, so there is no way they would ever evolve by happiness... until you realize Team Rocket's profession: Stealing rare Pokemon. The fact that some Pokemon know Frustration only cements this.
- The Female Rocket Executive has a Thick Club Marowak in both fights, which is frightening when you know what happened 3 years ago in a certain Pokemon tower and a Marowak...
- And finally, the fact that some Team Rocket members have pseudo-legendaries and some really rare Pokemon like Lapras, Aerodactyl, and Snorlax. The last Rocket Grunt you face in the Radio Tower has a Dragonite. The Final Executive? His last Pokemon is a Tyranitar.
- Mt. Mortar starts off with a surprisingly well lit cave, but as you go deeper, the cave gets darker, and the deeper you go, the music changes, until you go into the farthest part of the cave, where it is very dark, surrounded by some really dangerous wild Pokemon.
- The Trainer House boss battle. You enter a pretty cheerful Viridian City, and enter a large, pretty innocuous building, where everyone is having a good time. Then you enter the basement, and the music changes... to the Unown radio theme. The basement is dark, and seemingly empty, and your opponent isn't Cal this time, but another trainer called "SHF". You fight this trainer, who traveled all the way here just so he could battle the player. And the team rocket theme plays, and then you see his first Pokemon. A glitch Pokemon that uses the trainer sprite... at first, but if you try to use an item, it becomes a glitchy abomination of nature... The strange name "SHF"? Stands for Sinister Hooded Figure, the hack's creator, and he has a Missingno as his lead.
- Cinnabar Island's fate after the volcanic eruption. The city is covered by a huge mountain, with a rooftop embedded in the mountain. And the Pokemon center is nothing more than a shack with almost no power, as the inside is pitch black. And the Pokemon Center theme is replaced with the a more melancholy theme...Blue: Take a good look around you... A volcano erupts, and just like that, a whole town disappears. We can go on winning and losing in Pokemon. But if nature so much as twitches, we can lose in a second.
- Mt. Silver. What makes this stand out is that nearly every part of the game already has dangerous wild Pokemon, very powerful trainers, even more powerful bosses, and treacherous landscapes and dungeons. But according to Professor Oak, Mt. Silver is regarded as too dangerous for the standard trainer, meaning that after everything you have gone through, is child's play compared to Mt. Silver. And the revamped Mt. Silver delivers such delights: some of the single most dangerous wild Pokemon in the game, some of which are not commonly used by regular trainers, which can out speed or status you, or just outright destroy you. Not to mention that you are constantly scaling the mountain, even having to get past a gigantic waterfall, until you actually reach the peak of Mt. Silver, and every area in Mt. Silver you get past, the wild Pokemon can get much scarier, from Nidoking and Tauros, to Aerodactyl, Steelix, Electrode, Gengar, Alakazam, Crobat, Dragonite, and Tyranitar.
- Whatever lies beyond the alternate cave entrances within Mt. Silver. If the player character tries to go in one of these, they will immediately turn back, not going inside the entrance, unless it is the cave entrance that leads to the path to Red.
