Despite the reputation this game has garnered, it's still one of the darkest games in the Sonic franchise as the below entries will show you.
From the game proper
- Going up yet another level from his previous schemes, Dr. Eggman's plan in the game is to use the Chaos Emeralds and Solaris to gain control of time, space and all of reality forever. He's also a lot more of a No-Nonsense Nemesis this time around; banishing Sonic, Tails and Knuckles to the distant future as soon as they give him their Chaos Emerald as ransom for Elise's safe return, sets a runaway train to crash into explosives to cover his escape on Radical Train, and very seriously threatens to bomb Soleanna to the ground with the Egg Carrier if Elise does not willingly give herself up after Sonic helps her escape.Eggman: Sonic... shouldn't you save the train before going after me?
- 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.
- It's even creepier in the Japanese version. Dan Green is a brilliant Cold Ham in his performance, but there's just something about Takayuki Sakazume's inflection as that slow Creepy Monotone.
- Just Mephiles in general. Iblis is the more powerful and immediate threat, but Mephiles is just unsettling and filled to the brim with Paranoia Fuel. He prefers to get into people's heads, attempting to manipulate anyone he comes into contact with, successfully tricking Silver into almost killing Sonic and attempting Break Them by Talking on Shadow and Omega at different points in the story. That's not to say he's completely defenseless in battle; he can make multiple copies of himself, fire dark energy, darken the floor beneath him to hide in, and create his own dark minions to do battle with. And the worst part is that most of what he says is Metaphorically True; considering that Sonic is an Iblis Trigger, albeit not in the same way he implied to Silver, it's not a stretch to assume that he's presenting the truth in a less than accurate way to trick people into making the wrong decisions. Which then begs the question...how many details of Shadow's future cruxification did he purposely leave out?
- The insane laughter he makes after killing Sonic, without his mouth moving and with his head rolling back, is also incredibly unnerving... especially considering Mephiles, by making Elise cry to destroy its seal, now has the means to fuse with Solaris and consume all of time itself.
- The fact that Mephiles was actually able to kill'' Sonic is frightening enough.
- 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, the ruins of a modern-day metropolis leveled to the point where it's half-submerged in lava and regularly decimated by firestorms. Silver straight-up says at the start of his story that it's a bad place to live.
- In the final level, End of the World, there are dark-colored pocket dimensions with creepy reptilian slit pupils, known as the Eyes of Solaris. The dark red type warp mass from other locations to bombard you with containers, and the dark blue type sucks in everything surrounding it like a black hole, including you for an instant death. Oh, and if too many of them spawn at once? Space-time collapses in on itself.
- The End of the World and the fight against Solaris take place in a chaotic fusion of Soleanna's various places in a bleak purple limbo, that is evidently in the process of completely collapsing in on itself due to Solaris devouring both time and the very fabric of reality. It's especially eerie to revisit all the beautiful places you've visited in Soleanna when they've now been reduced to such a decimated and frankly wrong state.
- The beginning of the last story, with Mephiles grabbing the Purple Chaos Emerald as it floats towards him. Afterwards he slowly turns his head to the camera and faces the player all without saying a word, implying he's well aware of both the fourth wall and your presence.
- Not to mention that the knowing way he turns towards the camera and the creepy stare he gives implies that, despite not having a mouth, he's smiling; an implication supported by the fact that the reprise of his Leitmotif playing at the time is called "Mephiles' Smile" on the soundtrack. How effective a monster do you have to be when you can grin so frighteningly without even needing a mouth?