Anti-Climax: After a battle with the real final boss, there's one more level that repeats the chase scene gimmick already seen twice in Technology Tree. It's intense enough regardless, but still ends with a victory by cutscene.
Author Appeal: Snow. In reply to a question about why there's so much snow in the Special Acts, LakeFeperd said that it's because he doesn't see much snow in Brazil.
Bag of Spilling: Dr. Eggman almost gets the Chaos Emeralds from Sonic after Horizon Heights, but thanks to Tails they're only lost instead.
Color Failure: Tails at the end of the Moon Mansion Zone introduction cutscene.
Continuity Nod: During the final battle of the previous game, Titanic Tower could be seen separating into its next stage to provide extra launch for the Death Egg. In the final stretch of Storm Station Act 1, that very same segment of the rocket is seen stuck in the top of Parhelion Peak.
The badnik that harassed Tails for the better part of the previous game also turns up twice during Moon Mansion's third act, is the boss of Moon Mansion, and shows up a fourth time in the special act of Moon Mansion.
Corridor Cubbyhole Run: In Foliage Furnace act 3, there are several trains traveling through the area, and you frequently have to hide under the tracks or on platforms above them while you wait for them to pass.
Foregone Conclusion: As before, the Death Egg will still end up on Angel Island and prompt the events of Sonic 3. Well, Sonic can save Angel Island from landing in the sea in the Boss Rush, but that's just a "FAKE END".
What isn't foregone is that almost none of this game's other events have anything to do with Sonic 3.
Gameplay and Story Segregation: In Classic Mode, you can collect the Chaos Emeralds in Horizon Heights despite the fact that you already start with them and lose them after the boss.
Genius Programming: LakeFeperd works extremely fast. After only working on the game for eight months or so, the game was declared finished in October, extra zones, bonus features and all, and the only thing holding it from release was the unfinished soundtrack. Many people have theorized that he is in fact a robot, a hivemind of ten people, or using illegal workforce.
Giant Mecha: The huge segmented robots of Parhelion Peak, which were inspired by Sonic 2's Rexon. In that zone's boss battle, you assist such a robot in punching the living daylights out of another giant robot who has been hassling you with its laser.
A straightforward example of the fire-ice motif the original Trope Namer set is seen in Parhelion Peak's special act.
Helpful Mook: The orange giant snake robot in Parhelion Peak isn't hostile to Sonic and Tails. In fact, it not only is crucial to defeating Parhelion Peak's boss, but it even gives them a lift to one of the Egg Fleet's planes to help get them up to Storm Station.
Karma Houdini: Eggman, of course. The unnamed sphere badnik who stalked Tails in the first game, and survives this one too. The mysterious True Final Boss is probably one, since it's going to have a role in Sonic Chrono Adventure, and its defeat in this game was suspiciously anticlimactic...
Lethal Lava Land: Redhot Ride Zone, Foliage Furnace act 2, and Parhelion Peak Zone's special act.
Level Ate: Sugar Splash Zone. What with the giant piles of sugar, small piles of sugar that make Sonic run faster, and Sonic's animation when he eats it, the zone has been affectionately nicknamed "Cocaine Hill Zone," "Cocaine Coast Zone," and any other number of crack-related names.
Meaningful Background Event: Constantly. Anything eyecatching in the background has some importance. The meaning of a recurring symbol is later explained in Sonic Chrono Adventure.
Multiple Endings: There are three endings in the game — the normal ending, the bad ending (if the player has not collected all the Chaos Emeralds in Classic Mode), and the "Fake End" (seen by completing the Boss Rush). Needless to say, the normal ending is canon.
Moon Mansion Act 3 has one to Crisis City and the Special act has a nod to BTS's Fortress Flow Zone (Which Andy also composed)
Parhelion Peak's boss has multiple nods to Neon Paradise, another one of Maxie's songs (Which was eventually remixed by Falk for act 2, but originally it had an original track, now in Horizon Heights's special act instead)
Horizon Heights' special act has nods to both the PC and Genesis versions of Ice Cap Zone.
Storm Station act 2 is full of nods to BTS stages, plus Moon Mansion and Redhot Ride.
Redhot Ride's boss's intro has a nod to World's Largest Unicycle from BTS
Remixed Level: The special acts share their level design with the act they were unlocked in, but have many more hazards.
Reports of My Death Were Greatly Exaggerated: Remember that orby-robot-thing that kept harassing Tails in Sonic Before The Sequel, only to plummet from the sky after multiple defeats? Well, it reappears in Moon Mansion Zone. And it's only really dead once you beat it up three more times! And even then it may still live: It reappears in Moon Mansion's unlockable extra act.
Secret Level: Finding the gold star ring in each zone will let you access the special act for that zone.
Super Mode: Super Sonic is playable once all the Chaos Emeralds have been collected.
Super Not Drowning Skills: The Bubble Shield. Unlike the original games, if you're underwater when you have the bubble shield, you can't lose it if you get hit, meaning you don't even have to worry about losing it. However, one should note that the icon on the shield's monitor is actually a vertically flipped version of the original bubble shield's, so it could just be a deviation from the genesis bubble shield.
Averted for the Flame Shield and the pools of lava you can submerge yourself in at Redhot Ride, Act 2. Sure, the shield will protect you from taking damage under lava (you can't even lose it if you get hurt!), but you can still drown in lava with it equipped. And lord help you if you should lose the shield when above lava...
Unexpected Gameplay Change: Who doesn't brace themselves for a Super Sonic finale anymore? Only this time, Dream Dance Zone starts as this, and then turns the trope on its head in act 2, where you race through an obstacle course with normal controls while the True Final Boss stalks you. Super Sonic's even given a traditional life meter instead of rings (replenished by collecting rings regardless).
Variable Mix: Storm Station's boss music, Eye of the Storm, starts increasing in intensity the more damage the boss takes.
Moon Mansion Zone's boss has four alternating phases, each with their own track.
Weather Control Machine: Storm Station is this, which explains the storm forming around it and the existence of the special acts.