Revenge of the nerds

[Dr. BUGMAN]

I don't care about continuity one way or another. I'm tired of this farce that this numbnuts has some master plan when he clearly doesn't. All he needs is poison koolaid at this point.

[big_smile]

Gathering the Pinball Party events got me thinking. What's the origin of the spin dash? How is everyone able to do it? You'd think it would be a signature move for Sonic, and it's believable that Tails could've learned to do it by imitating Sonic, but Knuckles was able to do it before they even met. That means there's some history to it - perhaps as ancient as the Knuckle clan itself. Even little 6-year-old Cream was able to do it on her first outting, so maybe it's something innate to certain species of anthro. Or maybe it's a cultural thing they all learn to do as kids, like riding a bicycle. Depending on how young they learn it, I imagine it would make childproofing the house somewhat more involved.

I've wondered about this too, but I think the universality of both the spin dash and spin jump is just a case of developer laziness. In earlier games, characters like Espio and Amy couldn't spin dash/spin jump and had their own alternative moves. In Sonic Adventure, it looked like the spin dash was a Sonic only move (which is what it should have been from the start), although Tails and Knuckles could still spin jump. But then around Sonic Advance 2/Sonic Heroes everyone started doing it. Even Charmy could spin jump despite the fact that he's permanently flying.

[Jingles]

The spin dash is definitely a Knuckle clan tradition that was somehow passed down through generations, probably by an enemy of theirs out of spite, and eventually became common knowledge. Knux knew how to do it without any contact with the world below in S3&K, and Tails picked it up via imitation of Sonic. Maybe Vanilla taught it to Cream, but it was more likely Cream's dad seeing as Vanilla was unable to defend herself from being kidnapped at the end of Advance 2.

Rolling is probably seen as common form of bare-handed combat akin to kicking, but if you're holding a weapon (i.e. Amy in Advance 1) it is too cumbersome to rely on as your primary attack, and if you have extraneous appendages (such as whip-like tails) you'll have more experience using them anyways. I imagine rolling comes more naturally to animals with bodies suited to it, like hedgehogs and armadillos.

How does Espio do that spinning-top thing in Chaotix? He's able to enter it even when going down hills!

[Dr. BUGMAN]

How 'bout this: Both Sonic and Knuckles learned it independently via prolonged exposure to the Special Stage and it spread via Sonic's fame.

It'd also explain why Sonic didn't learn it well into his teens, and why the CD spindash is relatively rudimentary (the mobile remasters aren't retcons are they???).

[Jingles]

Just throwing this out there: Heavy and Bomb are totally pre-alpha builds of Cubot and Orbot. I imagine the Bomb enemy from Sonic 1 is an even earlier model.

I wonder what animals are inside those guys? Are they even considered "badniks" by Eggman?

[Dr. BUGMAN]

Ever think of where Knuckes got his shoes? I mean, none of his ancestors wore high tops, opting instead for sandals (and, erm, modern gloves), not to mention they look rather new. If he's isolated for his whole life, and effectively impoverished, how'd he get them? Perhaps they were a gift from Eggman; they do share his red and yellow and riveted-metal-plate aesthetic. Moreover they could've curried trust from Knuckles to better manipulate him.

(yes, I'm speculating on this of all thing, what of it)

[Jingles]

The shoes could have been brought to him by one of the flying animal buddies from the world below. Knux is thought of as being totally isolated before the events of 3&K, but there were plenty of other animals on Angel Island for him to befriend (and, as Runners confirms, he can speak to them without need for translation).

I suspect the gloves were originally designed as both a protective measure and punch-enhancer by the Knuckle clan (those guys sure were influential!) to be used in unarmed combat. Notably, Tikal's gloves don't have the fist-nipples, so non-warriors probably just wore them to prevent chafing and it caught on.

[Frieza2000]

the universality of both the spin dash and spin jump is just a case of developer laziness.

Well yes, that's probably the honest answer to almost every world building question you could raise outside of the emeralds and the history of the Knuckle clan - I was just inviting some creative problem solving.

(the mobile remasters aren't retcons are they???).

What about Sonic Jam? There's a mode where you can use the spin dash in Sonic 1!

The shoes could have been brought to him by one of the flying animal buddies from the world below.

Or made right there. They might've had their own little civilization going on, as evinced by Carnival Night and the Balloon festival + ski resort on Icecap.

[big_smile]

I've always wondered about Carnival Night. Was it part of the Echidna civilization or something Eggman whipped up due to his love of theme parks? And if Eggman made it, how come Knuckles didn't freak out (or about Launch Base for that matter?). Or was all the technology magical to the gullible Echidna and cemented his belief that Eggman was some sort of deity/holy man?

Regarding The Balloon festival + ski resort on Icecap:
In Station Square there is a guy who says he frequently goes snowboarding. So I think the Mystic Ruins has a ski resort, which Sonic gains access to via Angel Island, but the area is not a part of Iceap itself. Although y'd think a ski resort would have better access, but perhaps it has it's own station which is one of the destinations of the Station Square train.

Well yes, that's probably the honest answer to almost every world building question you could raise outside of the emeralds and the history of the Knuckle clan - I was just inviting some creative problem solving.

Personally, I treat the Spin Dash like the score and lives counters, but I like your creativity!

[Wombatwarlord777]

I've always wondered about Carnival Night. Was it part of the Echidna civilization or something Eggman whipped up due to his love of theme parks? And if Eggman made it, how come Knuckles didn't freak out (or about Launch Base for that matter?).

The answer concerning Carnival Night is probably that Eggman built it, but then you have to ask how the fuck he built it so freaking fast (I can look past the question of how he built it without Knuckles noticing, Angel Island's a pretty huge place and I imagine Knuckles mostly stays near the Master Emerald Shrine). I like Frieza's theory that there's a separate society of sentient animals / humans / whatever that developed independently of the Knuckles tribe and still exists on Angel Island, but then you have to ask why you don't see more developed places that clearly aren't Eggman's bases / industries. A big theme park would imply a large urban area. Maybe we just never go through it in S3&K?

Your question about Launch Base I think is pretty easily explainable. Again, Angel Island's a huge place, and unlike Carnival Night, Launch Base is clearly integral to his goal of getting the Death Egg airborne again. Eggman has a lot more of a motivation to get that place set-up toothsweet and besides, it's adjacent to the crashed Death Egg itself, so he probably has immediate access to all the raw materials / equipment he needs to set up his launch base (I honestly wouldn't be surprised if Eggman cannibalized non-essential parts of the Death Egg in order to get Launch Base up and running. If nothing else, it makes the damned thing lighter).

I've always been curious about the state of the Eggman Empire. Does it actually have significant territory and a subjugated population? Eggman's apparent easy access to resources and funding would seem to indicate that that's the case, but then in some of the games (like SA2 and Unleashed), his domain is piddling. In other games he might seem to have a big-ass flagship / armada / space station, but that's apparently it.

I honestly think the areas most firmly in his control are probably isolated islands, far, far away from other global powers like the United Federation. That might explain why he thought he could so easily conquer South and Westside Island, and why he seems to have easy access to resources while still itching to expand.

[Frieza2000]

I've always wondered about Carnival Night. Was it part of the Echidna civilization or something Eggman whipped up due to his love of theme parks? And if Eggman made it, how come Knuckles didn't freak out (or about Launch Base for that matter?).

Knux seemed to know his way around Carnival Night (or at least how to operate the lights, which uses the same button mechanism as all of his other traps, so it seems like it's native). We already have teleporters in Hidden Palace and Sky Sanctuary, fans, turbines, and pressurized water in Hydrocity, a vast network of lava pipes (too ingrained not to be native) suggesting thermal electric generation or at least steam power, and various sorts of automated doors, so the Echidnas were pretty technologically advanced (we know from Chaotix that they'd mastered the big ring portals too). It's just a different sort of tech than Robotnik uses. Other interesting note: some stage elements (buttons, springs, etc) are encased in ice in Icecap, suggesting they've been there since long before Eggman showed up. That includes elemental shield boxes. Perhaps the reason we've so rarely seen them since S3&K (other than magnet shield, which could be a human variant of lightning shield) is because they were an exclusively Echidna technology and they didn't start getting replicated until well after S&K.

Launch Base is an odd one. I think most of it was already there - there's an architectural clash between some of the elements.



These yellow towers look almost Arabian and were probably native. The red I-beam structures, the scaffolding, the zip lines, and all of the alarms, were probably the only things added by Eggman. He had told Knuckles that he was a scientist who had come to study the 'dragon egg' so he probably tolerated these minor additions, either on the promise that Eggman would clean up when he was done or knowing that he could knock it all down himself at some point.

Your question about Launch Base I think is pretty easily explainable. Again, Angel Island's a huge place, and unlike Carnival Night, Launch Base is clearly integral to his goal of getting the Death Egg airborne again.

I think Smile's point was that Knuckles is in Launch Base Act 2 and doesn't appear to be angry about what Eggman has done to the place.

In Station Square there is a guy who says he frequently goes snowboarding. So I think the Mystic Ruins has a ski resort, which Sonic gains access to via Angel Island, but the area is not a part of Iceap itself.

I checked the NPC script and the only mention of snowboarding is this guy:

Once my work's done, I wanna go snowboarding! It's a great feeling coming down that mountain!

He doesn't say where he goes. Obviously you're supposed to think of Icecap because that's the next zone, but I'm skeptical. Icecap is the only mountain visible in the area where Angel Island crashed. This guy may may go boarding on a snowy mountain in another part of the Mystic Ruins, or somewhere else entirely. That train surely connects to more places than just the Mystic Ruins.

I've always been curious about the state of the Eggman Empire.

I don't think there is one. That's his dream, the thing he's always on the verge of making a reality. In the meantime he just takes what he needs as he needs it. He probably jumps from secret base to secret base, has an army of bots and some vehicles in storage, and some accumulated resources, but that's. We discussed his funding toward the end of page 2.

[Dr. BUGMAN]

The shoes could have been brought to him by one of the flying animal buddies from the world below.

Or made right there. They might've had their own little civilization going on, as evinced by Carnival Night and the Balloon festival + ski resort on Icecap.

Yeah, it's a little ambiguous as to what the Knuckles clan is wearing isn't it? Tikal is no doubt wearing sandals, and 'ol Pachacamac is little less obviously is too, but your garden variety Knuckles warrior is even less yet. They resembles Pac's close enough, but with what appear to be either anklets or socks; they're also the same color as their fur like Tikal and Pac, too, whereas Knuckles' do not. More over the yellow "stripe" clearly wasn't always a stripe, but as thatt seems to be a retcon regarding the Uekawa redesigns, it's probably immaterial albeit worth bringing up. The point is, even with the redesign Knuckles shoes seem only themed after his antecedents' sandals. If they had the technology, why then did they opt for sandals?

Also, Eggman clearly knows how to make shoes as evidenced by the plot of Sonic Labyrinth. So it's not a huge leap in logic to think he couldn't make Knux's!

(the mobile remasters aren't retcons are they???).

What about Sonic Jam? There's a mode where you can use the spin dash in Sonic 1!

Yeah, but that's not on by default, is it?

[Frieza2000]

If they had the technology, why then did they opt for sandals?

That's the interesting thing about them. The society we saw 3000 years ago looked pretty primitive. Stone pyramid buildings, basic clothing, spears? Maybe some of what we see on Angel Island (such as electricity) was developed long after the remnants of the Knuckle clan went into the sky. Or maybe they just like to live close to the land. The legends say that the ancient society was prosperous and had abundance through use of the Master Emerald's power (or the Chaos Emeralds, depending on which legend) - it's never actually said that they were technologically advanced. We're only left to assume that they could create Hyper Ring portals prior to the fall because Eggman found the same portals in Neutrogic High Zone (and it's a good way to explain how they expanded their influence to Westside and Cocoa Island). They were also described as "a peaceful and happy society," with only a particular sect of elders/wise men trying to abuse the emeralds' power. Since the Knuckle Clan didn't have the emeralds before their fall, it could be that the ancient civilization is actually the Chao. Or, as Chris suggested earlier, the Knuckle clan rebuilt itself after the first fall, used the emeralds to prosper, then they ran amok and destroyed them a second time, after which Angel Island was created. Or maybe they took to the sky after the first fall and took one set of emeralds with them (the second set being sealed in the special stage), maintaining some contact with the surface through ring portals, then had their second fall on Angel Island itself.

The shoes being a gift from Eggman is totally possible but eminently strange. Of all the gifts to give to win his trust, shoes? I'd expect them to be booby trapped like the ones from Labyrinth.

No, spindash in Sonic 1 isn't on by default; I'm just joking around.

[Dr. BUGMAN]

I dunno, Flickies have mastery of Teleporter Rings, and they likely qualify as just barely sapient. It at most says the Emeralds -- or whatever powers that be -- ordains who can and cannot use them. Moreover, it's a common sci-fi/high fantasy trope that potent magic stunts technological growth.

As for the elemental barriers being incased in thick ice, well, Eggman/-robo's mech does just the very thing in that same zone to Sonic and pals in an instant, hazards in Wacky Workbench, too.

[Frieza2000]

I dunno, Flickies have mastery of Teleporter Rings, and they likely qualify as just barely sapient.

Before Smile clubs you, the animal friends are totally intelligent. But I agree with your point. Like I said on page 1, it's even possible that they're a naturally occurring phenomenon in the geographic region surrounding the Pillar (regular ring portals go to the special stage, but every Hyper Ring we've seen leads to the altar in Hidden Palace, including the one in Neutrogic High Zone, but that could just mean it served as a transit hub or a power source to sustain the links). Eggman eventually masters both types of ring portals, so it's possible to do with tech, but the Knuckle clan may well have done it with the emerald's power instead. That doesn't remove the tech embedded in Hydrocity, Lava Reef, and Hidden Palace, though.

As for the elemental barriers being incased in thick ice, well, Eggman/-robo's mech does just the very thing in that same zone to Sonic and pals in an instant, hazards in Wacky Workbench, too.

I had thought of that, but why would Eggman encase random springs and item boxes in ice? It doesn't slow Sonic down at all.

[Dr. BUGMAN]

That doesn't remove the tech embedded in Hydrocity, Lava Reef, and Hidden Palace, though.

Those switches were present in every island Eggman invaded:




He could've given Knuckles some DIY traps to install.

I had thought of that, but why would Eggman encase random springs and item boxes in ice? It doesn't slow Sonic down at all.

It slows him down as much as any typical badnik. What's more, Sonic can't rebound off of ice blocks like monitors and enemies, so there's some strategic value.

[Wombatwarlord777]

Was there ever an in-game explanation for the item monitors? I could have sworn that the Sonic 1 US manual said that they were brought along by Eggman to South Island as item caches, but looking at it just now that doesn't appear to be the case.

Could some sort of friendly entity be leaving them behind for Sonic's benefit? After Sonic 2, Tails might be the one responsible, but it doesn't explain the monitors prior to that. Maybe GUN does this in locations it knows it can't easily mobilize forces to aid local resistance groups? Maybe they're even leftover ancient tech?!

[Wombatwarlord777]

The shoes being a gift from Eggman is totally possible but eminently strange. Of all the gifts to give to win his trust, shoes? I'd expect them to be booby trapped like the ones from Labyrinth.

Perhaps the shoes weren't meant to sabotage Knuckles in case he started getting wise to Eggman's plan, but to track him with an embedded GPS chip or something.

In S3&K, Knuckles always seems to be in the right spot to impede Sonic and Tails's progress. For all we know, Eggman was monitoring Knuckles's movements the entire time, and if he happened to be in the same vacinity as Sonic and Tails (who were probably tracked via surveillance equipment installed into regular badniks), Eggman could tell Knuckles to quickly prepare a trap. Having Knuckles's new shoes be how Eggman traced him would be a fairly innocuous way to do so without raising immediate suspicion, assuming Knuckles Tribe technology really was relatively primative.

Also, Eggman's goal in Sonic & Knuckles shifts to stealing the Master Emerald. What better way to find that particular item than to see what locations its guardian frequents? And Eggman finds the Master Emerald pretty easily too in Sonic Adventure and Sonic Adventure 2. Even if Knuckles had moved the Master Emerald to the old outdoor temple after the events of S3&K to try and throw Eggman off in the future, that wouldn't matter at all if he were unwittingly still wearing the same, chip-ridden shoes.

[Dr. BUGMAN]

Also, wouldn't having metal plates on his shoes make him more conductive for electroshock? Those electrodes must have been for such a contingency.

[big_smile]

Also, Eggman's goal in Sonic & Knuckles shifts to stealing the Master Emerald. What better way to find that particular item than to see what locations its guardian frequents? And Eggman finds the Master Emerald pretty easily too in Sonic Adventure and Sonic Adventure 2. Even if Knuckles had moved the Master Emerald to the old outdoor temple after the events of S3&K to try and throw Eggman off in the future, that wouldn't matter at all if he were unwittingly still wearing the same, chip-ridden shoes.

In Sonic Runners, it stated that the ME was moved to underground temple (which is why Knuckles is able to go on adventures). Eggman only found the temple in Runners, so presumably he didn't know the location from Advance 3 to Runners, which makes unlikely that Knuckles has a chip in his shoes.

[Dr. BUGMAN]

Was there ever an in-game explanation for the item monitors? I could have sworn that the Sonic 1 US manual said that they were brought along by Eggman to South Island as item caches, but looking at it just now that doesn't appear to be the case.

Could some sort of friendly entity be leaving them behind for Sonic's benefit? After Sonic 2, Tails might be the one responsible, but it doesn't explain the monitors prior to that. Maybe GUN does this in locations it knows it can't easily mobilize forces to aid local resistance groups? Maybe they're even leftover ancient tech?!

I once hypothesized that the ring monitors were harvested rings badniks collected for the Special Stage. But of course that doesn't do much to explain the barriers, muteki and, especially, the 1UP monitors. The speed shoes monitors could be considered deliberate sabotage if you squint really hard.

[Frieza2000]

Those switches were present in every island Eggman invaded: ... He could've given Knuckles some DIY traps to install.

Not so much the switches as the entirety of Hydrocity and Lava Reef. I would argue that the network in Lava Reef was far to vast for Eggman to have set up in a day or two, and building Hydrocity would simply have made no sense. These were already there, whether they were constructed by the Knuckle Clan, other inhabitants of Angel Island, or they were left behind by another race the Knuckle conquered.

[big_smile]

Pengi (Crazy Penguin?) has been making some excellent posts on Sonic Retro, which I think the nerds here would like.

First up, a translation of the Bean and Bark characters profiles (translation by Hitlersaurus Christ):

Bean:
A woodpecker who appeared in the 1996 arcade game "Sonic the Fighters." He loves sports, and is particularly good at soccer. His special techniques are his spinning uppercut and bomb attack. His blue 2P color is BIN, the main character of the 1988 arcade game "Dynamite Dux", though Bean is his son.

Bark:
A polar bear who appeared in the 1996 arcade game "Sonic the Fighters." North Island's #1 snowboarder. He is blunt and quiet, but has a gentle and loving heart. He's actually a shy guy.

The second item is the discovery that Fang is half wolf, half Jeroba. This one is particularly fascinating as it explains why fang has a long tail and ears, plus only 4 fingers: These are all traits of the Jeroba.

[chriscaffee]

I'd like to revisit the Chaos Emeralds/Super Emeralds idea. I guess some minor Sonic Mania spoilers:

In Sonic Mania, if you are playing as Knuckles, you get a unique boss battle at the end of Lava Reef Zone which takes place in the Hidden Palace Zone emerald altar area. Here is a screenshot of the area:

https://vignette.wikia.nocookie.net/son ... 0819145007

Note there is some similarity to the "dead" Super Emeralds that appear in Hidden Palace Zone in Sonic 3 & Knuckles until you power them up in Sonic & Knuckles Special Stages:

https://files.shroomery.org/files/16-00 ... sonic3.jpg

Except the Sonic Mania versions appear cracked and damaged.

When asked about this Easter egg, Christian Whitehead tweeted the following:

"They're stone relics, created in their absence when the Chaos Emeralds once again drifted off into the Special Stage Dimension"

The tweet is very vague and could mean any number of things and Whitehead didn't elaborate when pressed further. Some possibilities:

1) These "stone relics" were naturally created when the Chaos Emeralds vanished.
2) These "stone relics" are man-made sculptures that were created after the Chaos Emeralds vanished.

Earlier in this thread, we discussed the idea that the Chaos Emeralds were split into two sets a long time ago and were re-united in S3K, then supercharged into Super Emeralds temporarily. After the events of S3K, the "Super Emeralds" are just now called Chaos Emeralds, and Hyper forms are just no longer used. For that theory to still work, based on Whitehead's tweet, the second interpretation is the one that makes the most sense. I'm not sure why the Super-Chaos Emeralds vanishing would cause a set of rocks to appear. I suppose anything is possible. However, thinking about the idea of the Super Emeralds being distinct from the Chaos Emeralds, rather than just powered-up versions of the Chaos Emeralds. Looking at his tweet again, what if the Super Emeralds were POWERED by the Chaos Emeralds? When the Chaos Emeralds vanished from Angel Island, then the Super Emeralds returned to their dead/rock form:

Rewind the clock back to the classic Sonic days. The Chaos Emeralds are a thing. There are seven of them. The Super Emeralds are also a thing. Separate things. There are seven of those as well. Here is the sequence of events:

1) The Chaos Emeralds are "asleep" (in the Special Stage) when Sonic arrives on South Island.
2) The Super Emeralds are physically present at various altars dotted around Angel Island and Knuckles guards them.
3) Sonic collects the Chaos Emeralds (via Special Stage) on South Island and returns them to the island. They retreat to the Special Stage.
4) Sonic heads to West Side Island.
5) Sonic & Tails collect the (same) Chaos Emeralds (via Special Stage) on West Side Island and keeps them.
6) The Death Egg crashes into Angel Island's lake, forcing it into the ocean. Knuckles happens to be near one of the Super Emerald altars when this happens. The Death Egg crashing causes a rift to open in Lava Reef/Hidden Palace Zone, and the Super Emeralds retreat to the Special Stage.
7) Sonic arrives on Angel Island with the Chaos Emeralds.
8) Knuckles, listening to Dr. Eggman's lies, mistakes Sonic's Chaos Emeralds for the Super Emeralds he had been guarding. (Remember that he confused Chaos Emeralds for Master Emerald shards in Sonic Adventure)
9) Knuckles ambushes Sonic and takes the Chaos Emeralds which also quickly retreat to the Special Stage.
10) Sonic & Tails re-collect the Chaos Emeralds.
11) Sonic & Tails enter Hidden Palace Zone.
12) The Chaos Emeralds summon or perhaps reveal the Super Emeralds from the Special Stage.
13) The Chaos Emeralds themselves retreat to the Special Stage.
14) Sonic can no longer transform into Super Sonic because the Chaos Emeralds are physically gone.
15) Sonic & Tails re-power the Super Emeralds one at a time.
16) Sonic &Tails can now transform into Hyper Sonic and Super Tails (with Super Flickies).
17) Sonic & Tails save the Master Emerald and Angel Island and befriend Knuckles.
18) Sonic & Tails leave Angel Island, leaving the influence of the Super Emeralds, and thus lose the ability to transform into Hyper Sonic & Super Tails (with Super Flickies.)
18) A surviving EggRobo and Mecha Sonic reactivate and attempt to steal the Master Emerald.
19) Either the Super Emeralds are still in Hidden Palace Zone and are fully charged and Knuckles going through the Special Stages is just a game element or the Super Emeralds have retreated, and Knuckles has to collect the Chaos Emeralds, re-awaken the Super Emeralds, and then re-power the Super Emeralds. Knuckles, on Angel Island, has the ability to transform into Hyper Knuckles.
20) After the events of S3K the Chaos Emeralds have retreated.
21) The Super Emeralds' power has retreated (permanently) leaving behind damaged "stone relics" as seen in Sonic Mania. The Hyper forms and Super Tails (with Flickies) are now no longer attainable. Only by collecting the Chaos Emeralds can super forms be unlocked.
22) Sometime after the events of (Knuckles') Chaotix, the Master Emerald is relocated to it's "original" shrine as seen in Sonic Adventure.

Overall I think I like this theory better than my other one. It explains why Knuckles and Sonic both have a set of Emeralds. It explains why Sonic and Knuckles cannot turn Super once entering Hidden Palace Zone. It explains why the Super Emeralds and Hyper forms are no longer a thing. It explains the appearance of the "stone relics" in Sonic Mania being distinct from the Chaos Emeralds that you collect. Either way, I think this is probably my new head canon.

[Wombatwarlord777]

While I think that makes a lot of sense, I'm still of the theory that the Super Emeralds are still just essentially souped-up Chaos Emeralds, although it has less to do with the events that transpired in the games and admittedly more to do with aesthetics.



The Emerald altar in Sonic & Knuckles has a strong botanical theme. The pedestals the Super Emeralds rest on feature ornate stem- and blossom-like details, with the Super Emeralds themselves are situated like ripened fruit. Coincidentally, the Chaos Emeralds in their original, octagonal forms had a passing resemblence to plant seeds, which is more or less their function in the game to give physical form to the Super Emeralds. The Super Emeralds are just different forms of the Chaos Emeralds under this arrangement.

We also have to consider that it's likely that the Master Emerald itself seized the Chaos Emeralds from Sonic, Tails and Knuckles in order to form the unpowered Super Emeralds. Interestingly, the Master Emerald also displays a degree of sentience / clairvoyance in Sonic Adventure, when it advises Knuckles to look for its last remaining fragments aboard the Egg Carrier. Interestingly, it wasn't even fully formed when it was able to do this, nor did it contain the souls / essences / whatever's of Tikal and Chaos at the time. This indicates that the "intelligence" of the Master Emerald has to come from somewhere else. Without any evidence to the contrary, we might conclude that in a world full of ultra-dangerous, high-energy rocks, the Master Emerald is unique in that it appears to innately possess a sort of free will and / or consciousness, at least in relation to either powering up the Chaos Emeralds or (in the case of Sonic Adventure 2) neutralizing them. You could also argue that it's the Hidden Palace Emerald altar that has the necessary circuitry to take the Chaos Emeralds and power them up, but that doesn't explain what the Master Emerald was doing in SA1.

So, during the events of Sonic 3 & Knuckles, the Master Emerald somehow detected that Angel Island / the world was in grave danger (or that it had come under great threat multiple times in a relatively short period), and transformed the Chaos Emeralds into Super Emeralds to allow Sonic, Knuckles, and Tails to transform into Hyper Sonic / Hyper Knuckles / The Flicky Whisperer and save the day. The Chaos Emeralds gave up their physical form and powers to serve as vessels for the increased powers of the Super Emeralds, which coincidentally had enough innate power to also serve as portals to the Special Stages. There the gang gathered enough additional ambiant Chaos energy to complete the transformation (unlike the initial seven Special Stages, in which the prize was a physical Emerald). After everything in S3&K wrapped up, the Super Emeralds used a portion of their energy to revert back into Chaos Emeralds and scattered, having gained enough additional energy to gain their larger, diamond cut forms. The leftover energy preserved the Super Emeralds' physical forms, but left them with no powers. I suppose you could argue that this whole process only happened once if Knuckles didn't need to gather Super Emeralds during his story.

The idea that the Super Emeralds in Mania are actually just stone replicas might make sense, but it really, really rubs me the wrong way. I like their appearance in the game, though, in that it acknowledges their role in Sonic 3 & Knuckles while also implying that their role has been completed and that they are not likely to come back.