There's nothing really that scary about Doki Forest, since the adults in Panselo don't mind their kids going to play there, and they're all shown to be relatively safe. So if you haven't played the original game, it's quite a surprise when it turns out that the village in that moment isn't safe, as a spaceship seemingly appears out of nowhere and shines a beam over it. Then when Gail and the kids return, everyone is gone, even the animals.
To emphasise how serious the situation is, you have to make your way back through the forest right after the abduction while the usual cheerful music is replaced with an eerie ambient noise, and there are no enemies which makes the place seem emptier.
It's scary for those that were abducted as well. Just imagine that you're waiting for your family to come home, only to be taken away and put in danger while you have no idea if they're safe or not. It gets even worse with the later reveal that those still on the planet are in more danger.
The Sand Drifts can be quite creepy, since there's no overworld music but instead the sounds of wind blowing, which carries over to the enemy encounters. Some areas have quicksand which is hidden well enough for you to walk into, and you might not have the Lifesaver at this point so the sudden drowning animation can be a Jump Scare.
Speaking of jump scares, the sudden appearance of a Dragon Snare is quite alarming. The only hint you have to their presence is a small flower, and the noise they make upon coming out of the ground is very sudden and frightening.
Daea is a nice-looking place with cheerful music, but you learn early on in your arrival at the city that many of the guards have been put under mind control, indicating that there's something going on that most of the citizens are completely unaware of.
When you first see the castle, a mysterious figure in a red cloak who doesn't look human is seen for a few seconds before disappearing, further adding to the fact that something isn't right.
After Gail, Thomas, and Bart fail to get into the castle and try to think of another way, they decide to spend the night at the inn. The usual music for whenever Gail goes to sleep plays... but before she wakes up, there's some dialogue of Thomas being visited by some of the brainwashed guards, who then beat him up and take him away. If you have no knowledge of what happens in the flash game, you might think he's ended up brainwashed himself rather than simply imprisoned.
To get into the dungeons, you have to travel through the sewers, which are dark until you can find the light switches. This wouldn't be that scary if not for the fact that there are enemies that can catch you off guard, including Fire Fish and slightly smaller versions of the Slargummy.
One of the non-brainwashed guards you meet in the dungeons describes how most of the others got mind controlled, by being restrained while a device of some kind is put on their heads, and also says that if they catch you, then it's over. Good thing they're only interested in doing it to other guards...
Towards the top of the towers, you meet the mysterious figure from earlier, who turns out to be Katash, the leader of the Kobolds. There's a brief moment where his ship can be seen in the background, implied to have been there for a while but invisible to everyone, and he summons a smaller ship during his boss fight, making him seem even more out of place than the other bosses you've fought so far by getting the point across that the Kobolds are aliens.
Even worse, it's hinted by his second encounter and some dialogue from Birdy after she's imprisioned that he isn't actually working with the Astral Empire or the space pirates, but instead someone else who is strongly implied to be one of the Phoenixes depicted in the Royal Archives who grew wings. We never find out who this is or what his goals are.
The Reveal that Earth is in danger, as the Astral Empire intends to not only invade it but take all of its resources, resulting in all life on the planet dying. It's bad enough for Bart to say that the abducted villagers, who were taken away to be sold and preserved as a rare species, are actually safer than everyone down on Earth is.
The optional dungeon of the Subterra has radioactive versions of the Gummy (and a Slargummy that is fought as a boss later), as well as Mimi Toads, which can turn invisible, making them harder to fight.
The Scorched Lands. The overworld plays a droning noise which increases in intensity during encounters, some areas have lasers that will make a lot of noise as they shoot anything in their way, and the enemies are some of the most dangerous in the game. It really is a place with Everything Trying to Kill You, and you'll even see the bodies of fallen guards to show how bad it is.
Ghouls are skeletal-looking robots that walk like zombies most of the time, but there are some that are missing their legs and still try to attack you from where they're stuck on the ground. There's also many that are completely still, and it's hard to tell whether they'll suddenly come to life or not. As a nod to the original flash game, there is one room that's completely empty except for a box from which a ghoul sprints right at you, and if you use a bomb or charged attack to destroy the box, it will come in from the door behind you instead.
Mole Mines are small bombs that come out of the ground and explode whenever it touches something, which will usually be Gail if she doesn't jump or run the other way in time.
Remember the Wrecker that Thomas made you fight? There are more of them here, and they're just as dangerous as that one, if not more due to the environment being different.
The most dangerous enemies are the Wendigos, which the guards at the Last Wall will tell you that you should run from as soon as you see one. They're not kidding; their defense is so high that you'd have to use a lot of attack-boosting items to do any damage to them at all, and they can seemingly teleport or turn invisible. What's worse is that some overworld encounters will place you right in their line of sight, and it's a scramble to climb up the walls out of their reach. There's also one in the railway station (which you can use to get to and from Daea's Aqua Line) and in the Ancient GEO Base, both of which are darker and can make you feel like you're in a horror movie as you try to stay away from them.
The Mul Caves, while not as bleak as the previous area, can still be scary for anyone with a fear of bugs, as there are many crawling around the place, not helped by the number of nests scattered about.
At one point, the bug's queen Ariadne, who is much bigger than the rest, attacks Gail, trapping her in webs and taking her to the storage area. The noises heard as the screen fades to black as well as Bart's dialogue after freeing her imply that she was bitten and likely only survived the venom due to being a Phoenix, which she didn't know at the time. Good thing fighting Ariadne is optional...
It's not as bad as the Scorched Lands, but the lack of music in the overworld after you leave the Mul Caves is still unsettling.
The S.P.H.E.R.E is guarded by structures called Megaliths, which fire at anything that comes into their range, and can't be stopped until you've made your way past several of them into Pristine City and had the Spheralis assembled. It doesn't help that they make loud noises.
In E.D.E.N, you find a room with large glass orbs containing Trolls and Harpies, and in one of the rooms past that you'll find a Chrystalis, which you'll need to take so you can use it to unlock doors. As soon as you take it, the sound of glass breaking can be heard and the eerie background music stops. When you go back into the room, some of the orbs have broken, and the room after that has you forced to fight the Trolls and Harpies that escaped. It's never made clear just what caused them to escape, since they were implied to have been in stasis before.
In the room just before the Point of No Return, you see a large, humanoid figure with wings that the computers explain is an alien being that some people called "Adam", from whom the Phoenixes (and possibly other lifeforms) were created from. It's best not to think about what could happen if he broke free...
Adam's flesh is still regenerating, even while it sleeps. In some rooms they have tissue samples locked up, tissue samples that look like green crystalline growths with circuit patterns. Like the ones appearing in certain rooms of E.D.E.N. ...
Mother Computer has been overseeing the various projects to help protect Earth as well as make it habitable again, but she's also still had Phoenixes created long after the Great War, with no explanation as to why, and she also doesn't like the idea of them being anything more than living weapons, as after revealing to Gail that she herself is a Phoenix who was stolen, she tries to kill her when she refuses to go back into stasis.
Both her form here and her earlier form in the Royal Archives have frightening appearances, the second one even more so for being darker in colour and bearing more resemblance to a skull.
In the next room, Gail is cornered by the security, which seemingly transports her to an area that is red with black symbols in the background, where she has to fight against a shadow version of herself that can multiply. The intense music makes it even more frightening. Afterwards, it's revealed to just be an illusion from a projector much like the ones the old GEO dungeons used, and the shadows were actually just robots, but it's never explained why whoever designed the security to the Pheonix vault felt the need to involve illusions where you have to fight yourself.
Bart reveals that the Phoenixes are extremely powerful, and that they actually caused most of the damage to the world that forced everyone to leave the planet or live underground. Despite this, and the fact that there are implied to be thousands of Phoenixes here due to Mother Computer's continued creation of them, they are still needed to prevent the invasion. And if you lose to Katash when he fights you again, just one Phoenix is enough to defeat him and the other Kobolds he brought with him.
The ending, while mostly hopeful, reveals that while the invasion was stopped, the Astral Empire haven't given up and are interested in taking the Phoenixes for themselves...
