Just about anytime something dark happens, the music becomes distorted, which is similar to Yandere Simulator when Yandere-chan becomes insane from killing people. The music changes as the series progresses.
The discovery of Gareth's body in his classroom. All of the students just stare at it in horror and barely have anything to say. His "suicide" note is actually pretty sad.
Sam and Taurtis hiding from ChanYandere's house. When she wakes up, she goes down to grab a snack. She returns.... with a knife with red liquid all over it.
Sam, Taurtis, their dates and Dom going into the school at night. The bell starts ringing like crazy, changing every time. Then Sam looks out of the window and sees Gareth's ghost. They step out of the classroom and find blood in the hallway. Everyone sees him and they all start running and hiding from him. It gets even worse when they see him on the rooftop with rope in his hands.
When Sam and Taurtis go into their apartment, an anvil nearly kills Sam. The previous night, they had spotted the Yakuza through the window, looking for them. They looked through a chest and found a fake suicide note, claiming that Sam couldn't live with Sookie's rejection.
Sam telling SirCutieYuki that he and Taurtis aren't her prom dates anymore. Yuki takes Sam outside and pulls a knife on him. This is the first hint that Yuki isn't who she seems to be.
The second half of the Halloween Episode. Sam, Taurtis, and Grian are forced to stay in the high school and they find all sorts of creepy things happening. Blood starts appearing everywhere, signs with creepy messages pop up, and the guys keep encountering Gareth and Salex's ghosts. When they go back to the entrance, they find three stool with three long nooses hanging over them with blood dripping from the ceiling.
Sam spending a day without Taurtis. During gym class, he finally snaps, proclaiming that Grian is Taurtis and chases him down into the kissing shed. The next day, he goes on with his delusions and forces Grian to play as Taurtis and even threatens to stab him with a knife if he doesn't do what he wants.
For the Christmas Episode, Sam and his friends enter the school to chase off The Drinch. When they walk past their original homeroom, they see Gareth's ghost who calls them in for "role call". Out of fear, JTheStar, Sam, Taurtis, and even Grian go inside the classroom. It seems somewhat normal until he says that he's going to find who killed his wife. He grabs some rope and slowly walks toward Taurtis. Everyone responds by running out of the room in terror.
The Snowman. He seems like an innocent small snowman who asks for a little bit of food. However, the more food he eats, the bigger he gets. He starts asking for human flesh, which leads to Hidden being fed. Sam and Grian realize what they've done and try to find a way out of the situation.
Paul Blart's fate. He reveals that he killed Yuki's father and is chased into the theater by her. When Sam and his friends go into the back room and find his head.
In Tokyo Soul, Professor Geo's face begins to morph exponentially each day after he first clones Taurtis. By episode 24, it looks like a jumbled, twisted mess, with a big Slasher Smile that could make your blood curl.
Much of episode 15 is unnerving too. The clones are being processed through a machine that presumably kills them, and over a dozen are trapped in the pool. Cut to Geo approaching the real Taurtis wearing the face of a clone he had skinned. To make matters worse, all the clones scream for help, many calling out to Sam as if they remember him, suggesting they all have the real Taurtis' memories.
The finale of Tokyo Soul is pretty horrifying. Sam and his friends return to their universe, but they find their house as the only thing there. They have nothing in the house and no one else is there. Cthulhu reveals that the Minions took over the universe and possibly killed their friends and destroyed their homes. This also doubles as a Tear Jerker because Sam and Grian realize, to their horror, that they are responsible for the universe ending and the main gang is all alone with each other as company.
Sam posts a video talking about how creepy people have been impersonating him and other Minecraft users in order to lure unsuspecting kids.