From the game proper
- Mephiles the Dark's introduction. He slouches over and walks as though a puppet on strings with his creepy staring eyes, able to talk without moving his mouth, all with this music playing.
- At the start of the last story, Mephiles appears out of nowhere and instantly kills Sonic. Even though Sonic comes back to life eventually, it still happened.
- This game is the first, and thankfully only, to feature a realistic-looking Eggman so far. Unfortunately for Eggman, he was never meant to look realistic in the first place, and therefore attempting to cash in "serious, realistic-looking next-gen games" only resulted in Eggman falling deep in the Uncanny Valley.
- The Mephiles boss fight involves him summoning an entire swarm of mini-Mephiles which will dogpile Shadow while making creepy, high-pitched noises.
- Crisis City, a metropolis leveled to the point where it's submerged in lava.
- In the final level, End of the World, there are dark colored orbs with creepy slit pupils known as the Eye of Solaris. The dark red type bombards you with containers and the dark blue type sucks in everything surrounding it like a black hole, including you.
- The End of the World and the fight against Solaris take place in a chaotic fusion of Soleanna's areas in a purple limbo, due to Solaris devouring time itself.
From the Let's Play by pokecapn's posse
- "All the bacon in the world couldn't save you now..."
- Near the end, Kung-Fu Jesus starts chanting song lyrics in a Creepy Monotone.