The Wither Storm, a Wither that absorbs the surroundings around it to grow into a massive Eldritch Abomination and then proceeds to level, kill, or consume everything and everyone in its sight.
If you thought the outside was terrifying, in Episode 4, you go inside of it, finding its victims in a nightmarish state throughout its body. When you reach its heart, Combat Tentacles sprout out of everywhere and try to kill you until it sprouts three heads out of the inside of its body to attack you with.
Additionally, even if you aren't pulled into the Wither Storm and manage to escape it, exposure to the thing can give you a deadly sickness or complete amnesia.
The White Pumpkin of episode 6. Until now, your threats have been essentially mindless beasts, or a group of thugs who never actually kill anyone that we see. Now you have an actual person killing named characters in cold blood to acquire an artifact. An artifact that Jesse's group has one of.
The methods of murder are especially creepy. TorqueDawg is shot by poison arrows and dies slowly. Sparklez is suffocated in sand. Lizzie or Dan are either mauled by spiders or killed by the White Pumpkin themselves; which one it is and how they die are indirect choices you probably wouldn't even know caused it without replaying or looking it up online.
After Sparklez is killed and everyone realizes they are trapped in the mansion with a killer on the loose, they see that the portrait of Sparklez now has a giant red X on it like TorqueDawg's. Seeing how the two of them are right next to each other, everyone looks at the next portrait in line and sees that it is Ivor. Thankfully this presumed killing order was proven wrong, but still all Ivor could do at the prospect that he could be the White Pumpkin's next victim is give a simple "Well, I guess I'm next then".
PAMA in episode 7 is surprisingly creepy, using Redstone Chips to literally read about the lives and memories of those who are chipped and control their every move. It was designed by the Old World builder, Harper, to be an efficiency machine. However, it became too powerful and began to expand its resources to people as well, and is now obsessed with making everyone "useful". Everyone chipped by PAMA share PAMA's mind, have bright red eyes, and tend to speak in creepy unison.
Then, towards the end of the episode, Petra or Lukas will be forced to fight you while under PAMA's control to stop you from destroying PAMA's main control device. Throughout the fight, PAMA will say many creepy things to shake the player, even speaking about Reuben's death. The whole fight tinted in a bright red light helps in making things intense and scary.
PAMA:Why keep trying, Jesse? You will only fail. Just as you failed to saveReuben.Just as you failed to lead your friends back home. You will fail to defeat me.And Axel, Olivia, and everyone on your home world will soon be made useful.
In Season 2, there's the Admin. He's far too powerful for Jesse and company to simply attack him physically (which is how all previous enemies were dealt with, if you think about it). Also, all previous villains were either powerful forces of nature (or something like it, such as the Witherstorm, and PAMA to some extent) or crazy people with issues (such as Aiden to some extent, Cassie, PAMA to some extent for the given value of a person, and Hadrian and Mevia), but the Admin gives us both in the same package. Seriously, he's terrifying.
As if he couldn't get any worse, in episode 5 of season 2, one of the first things we see him do is either blow up all of Champion City with a clap, or strangle and kill Xara (if you didn't give her the bed), right in front of Axel, Olivia, and Stella when Axel and Olivia talk about trying to leave. Stella collapses to her knees in sheer shock upon this sight, and Jesse and gang are horrified.
