The trash heaps in Flying Battery Zone, containing pieces of busted-up badniks. It's quite unnerving to see familiar enemies missing eyes, limbs, or even their whole face.
The fact that the miniboss for the zone is a crusher. When this inevitably fails, Eggman attempts to drop Sonic out of the ship along with the trash.
Oil Ocean Zone Act 2. The oil in the rigs start emitting toxic fumes around the zone that get thicker and eventually clouding it and draining your rings once it's thick enough. You have to find switches to clear the fumes for a short while. Small wonder, since this is based off Sandopolis Zone Act 2, one of Sonic 3 & Knuckles' biggest sources of Nightmare Fuel, with the music having similar undertones to boot. Finally, the boss is a submarine shaped like a giant Octus badnik.
Hydrocity Zone Act 1's boss. You're chopping Eggman up with a propellor. Granted, he tried to do exactly that to Sonic, Tails, and Knuckles back in Sonic 3 & Knuckles, but still, thank God the game doesn't take itself too seriously.
Titanic Monarch Zone Act 1 has menacing Background Music and banners with Eggman's likeness on them that make you feel like you're running through either Nazi Germany or Soviet Russia. Act 2 features stained-glass windows of his likeness along with echoing, foreboding music, and portals connecting to other locations within the Titanic Monarch littered everywhere.
The normal Final Boss can give players a shock on their blind run. After going through a long hallway, suddenly the background lights up in flashing warning signs and the opening seconds of the final boss music, "Ruby Illusions", which sounds like a klaxon blaring. What comes is a frantic fight where the player not only has to deal with Eggman, but has to survive against upgraded versions of the Hard-Boiled Heavies. It really gives off the impression that Eggman isn't screwing around this time. Also, the final boss music also has laughs similar to the infamous boss fight music from the US soundtrack of Sonic CD.
The reworked Metal Sonic fight in Plus changes the final phase of the fight to Metal Sonic using the Phantom Ruby to turn into his final boss form from Knuckles Chaotix. Already terrifying by itself, Metal Sonic's new death animation has him shatter to pieces.
The Stinger for the normal ending for Encore Mode brings back the tradition of the game's villain, in this case Heavy King, juggling the emeralds that the player failed to get, with Heavy King looking down on the defeated-looking protagonists that finished the mode. Oh yeah, it also plays the laugh from the bad ending ofSonic CD, just for punctuation.
"Ruby Illusions", which sounds like a klaxon blaring. What comes is a frantic fight where the player not only has to deal with Eggman, but has to survive against upgraded versions of the Hard-Boiled Heavies. It really gives off the impression that Eggman isn't screwing around this time. Also, the final boss music also has laughs similar to the infamous boss fight music from the US soundtrack of Sonic CD.