Spoilers Off applies to all Nightmare Fuel pages, so all spoilers are unmarked. You Have Been Warned!
- Eggman's plot this time around is to use a machine that borrows energy from the planet to power his machines. However, once the Deadly Six escape his control, they use it to drain the life out of the planet and enhance their own abilities. Amy and Knuckles do eventually succumb to the effects of the machine further into the game...
- Sonic attempts to save a bunch of animals trapped in a plummeting capsule in the opening cut-scene. He misses and then he and Tails are promptly distracted by their ship being shot down, completely forgetting about their animal friends.
- The impact is somewhat lessened by the fact that Sonic Advance Trilogy had capsules that dropped from the sky in addition to the fact that the dropped capsule is the one in the first stage thanks to the subsequent cutscene, with all of the animals being rescued just fine.
- Then there's the rather violent quotes that refer to strangling, being skinned alive and even genocide. In a Sonic game!Eggman: "As long as I can still strangle a Zeti, my hands are fine."
- Eggman, when betrayed by the Zeti, is so pissed off that he ends up going to a VERY dark place with his threats. The severity of his mood and words are so off-putting that Sonic and Tails are shocked silent. Not since Sonic Adventure has Eggman been this ferocious and genuinely frightening. What's more is when Eggman makes his last threat to Zavok and Zazz, their facial expressions actually change from amused to surprise (mild for Zavok supposedly and rather clear shock from Zazz). It didn't look like either of them were smugly smiling at that moment, they were surprised that Eggman went there with his threats.Eggman: "I will destroy everything you love and make you watch!"
- Speaking of Eggman. Later in the game, he proposes an idea to Sonic about causing the Lost Hex to implode as a way of defeating the Deadly Six, basically saying he's willing to commit genocide just to kill his enemies. And the fact that he can so offhandedly suggest this in such a casual way paints the doctor in a whole new frightening light.
- Also, why did Eggman team up with his worst enemy to defeat the Deadly Six? Just so HE could KILL Sonic HIMSELF.
- Finally, when he does get complete control of the situation again, he upstages the Deadly Six as a villain and uses a mech that is powered by a lot of energy that was stolen through the extractor. Imagine how many living beings lost their life force just for the cape of that thing.
- In the 3DS version, said mech can make a miniature black hole that kills in one hit, devouring Sonic if it connects.
- To a lesser degree (given how it's laced with his typical Faux Affably Evil whimsy), there's what Eggman says regarding the damage done by the Zeti, hammering in how he fully acknowledges the energy used to power his mech was taken from a planet sucked dry and he doesn't care:Eggman: Pity about the damage done down there, but there's still enough left for me to conquer.
- Pretty much everything about Zazz. He's feral, savage, always has a crazy expression on his face and is constantly on the verge of a nervous breakdown, revels in violence and destruction, makes sadistic and graphic threats during his fights, and the sheer sadistic glee with which he taunts Sonic and Eggman about their home being destroyed makes him arguably the scariest of the Deadly Six.
- Zor's "death" by falling in lava wouldn't really count as Nightmare Fuel by itself as it's a common way to off an opponent, but the fact that he welcomes it ramps up the creepy factor to much higher levels.
- It's shown in the later stages of the game that Sonic well and truly DESPISES the Deadly Six for what they did, even more so than he'd ever feel about Eggman. The first moment this is shown is when he quietly curses them after Tails is torn away from him, and later, once he sees the result of that kidnapping, he's really close to losing his patience outright, and not at all willing to let them get away with their crimes all throughout.
- Zavok, when fighting you, falls deep into Surprisingly Creepy Moment territory with his Enemy Chatter, going from "I'll shatter you, your friends and your planet!" to "It will be hard for you to joke with NO TEETH. I'll savor your every scream and FEAST ON YOUR FEAR!!!" in the span of a single stage and then taunting Sonic about the implied genocide of his friends, family, and planet in the stage before their second encounter.Zavok: "Your fate is to be destroyed! Why won't you just accept that, lie down and die?!"
- The enemies in the Hidden World Zone 4. Instead of the usual Badniks, they are Pac-Man-like floating mouths, except covered in fur, having More Teeth than the Osmond Family and instead of eyes they have creepy black cross-shaped slits. What exactly they are is never explained, though in the game files they are called Baku Baku (Japanese for Chomp Chomp). Since the level features a gimmick of jumping between bubbles containing spike balls and Baku Bakus, the player has to carefully aim Sonic to the next bubble while being chased by any released Bakus, with the only way to attack them being aiming the iron balls at enemies. But the real nightmare comes at the end of the Zone, when Sonic is chased by a gigantic Baku Baku, which has to be killed to finish the level. It takes multiple spike balls to kill it, and its skin is so tough that the only vulnerable place is its open mouth. With the player also being chased also by smaller Bakus, having to avoid any spike balls that bounce around, lack of checkpoints and the slow level scrolling, this fight already beats any of the Deadly Six bosses in terms of scariness. But the Fridge Horror kicks in when you realize that, despite looking like flesh beings, the Bakus drop animals like Badniks. While could be just a gameplay mechanic to reward the player, or they could be some kind of robots, the boss version pukes a whole bunch of animals from its mouth every time it takes a hit, implying a much more disturbing explanation...
