Chaos has a blue body and green eyes— just like Sonic does. And those things on Chaos 0's head look like Sonic's quills.
In E-102's story in Sonic Adventure, his perspective on good and evil becomes challenged when his brother, E-103, stares at him pleadingly, an image that seems to haunt him. In short, it caused a change of heart. E-103's designation is Delta (Δ), which means "change in" when applied to mathematics.
In Sonic 3 & Knuckles, the Master Emerald was in the Hidden Palace zone. But in Sonic Adventure, it's in its shrine on the outside. How did this happen? Why did this happen? After Robotnik told Knuckles that Sonic sought the Emeralds for immoral purposes, Knuckles hid the Master Emerald just as he did with the 7 Chaos. After Robotnik was beaten by Super Sonic, it's possible Knuckles just returned the Master Emerald to its original shrine; the last we saw of it in Sonic's ending was that it fell out in the open of Angel Island, and we never saw Knuckles take it back to the Hidden Palace, and perhaps he couldn't, considering we don't know how much damage Robotnik caused it when he broke in.
About the Rashomon style of the storylines: everyone's personality is subtly shaded to be more like the viewpoint character's (ie. everyone has more of an attitude in Sonic's story, Sonic is more polite in Tails' story, et .).
Not to mention, the outcome of the battles between playable characters changes depending on who you're playing as, furthering this point.
Also, there's an interesting contrast between how Eggman acts in Sonic and Tails' stories. To Sonic, Eggman is a loud, hammy doofus and Sonic isn't afraid of him in the slightest. In Tails' version, however, Eggman's dialogue is a lot more subdued and sinister, giving him a very intimidating vibe. This becomes Fridge Brilliance when you take Tails' Character Development into account.
When playing in Adventure Mode after beating the game, it's always daytime except as Gamma, when it is always night (at least, in the Dreamcast version). Why is it different for Gamma? Because he dies the following day.
In Knuckles' story, he sees Gamma nearby the Master Emerald altar, but Gamma doesn't visit this area until later in the game. Seems like a continuity error until you realize that as Gamma makes a beeline for Eggman's jungle base, it means he's collected Froggy at this point, and is currently in a flashback. Tikal gave Gamma a vision while taking control of his body to lead Knuckles back to the Egg Carrier.
Either that, or Gamma had a flashback in a few seconds real time, and the Master Emerald altar simply was along the way.
Tikal giving Gamma a vision seems a random and superfluous act compared to the actual heroes, until you realize that in his own story, Gamma was Eggman's most pivotal minion in helping power Chaos and was seconds from destroying Sonic (who was destined to stop Chaos and save humanity) had he not gained a conscience. Tikal's conversation with Gamma mostly consists of subliminal claims of good will ("I see you are not one of them." "My hope is that one day we will all understand one another.") as if to try and bring empathy from the droid so he won't be able to fulfill his duties to Eggman.
Bar a couple of seconds, Tikal also doesn't seem the slightest bit creeped out by Gamma's appearance. According to later sources, her tribe's war was against the Nocturnus Clan, who created the Gizoids to help in their conquest. This gives her first comment towards him more meaning. Tikal's seen plenty of robots, she's just glad Gamma isn't one of those robots.
Or, since the scene between Gamma and Tikal in the past didn't actually happen, being a fabrication by Tikal, it didn't realistically depict what her reaction to his appearance would have been like.
This game is where the main 5 characters of the Sonic series (Sonic, Tails, Knuckles, Amy, and Dr. Eggman) were radically redesigned and were even given eye colors. Those eye colors actually tell us one small thing about them. Sonic's eyes are green, the color of an emerald, because of his constant use/involvement with the Chaos Emeralds. Tails' eyes are blue, the color of the sky, because A) He can fly using his tails and B) he can fly his airplane, the Tornado, making him the most likely to be airborne. Knuckles' eyes are an uncommon eye color (purple) because he is one from an uncommon species (which could also explain why Tikal's eyes are blue; it's because echidnas were common during her time). Amy's eyes are a brighter shade of green than Sonic's because green eyes are said to be the most attractive, and she gives a lot more of her romantic feelings to Sonic than vice versa.
Amy is pigeon-toed and has a short stride, so it makes sense that she moves fastest by taking giant leaps.
Dr. Eggman still doesn't have an eye colour (just his dark blue goggles), but he has become more egg-shaped, and this was where his name was officially changed from Robotnik to Eggman in the US and Europe.
In Knuckles' stages, you can touch the glowing orb (Tikal) to show you where the Master Emerald shards are. The reason the orb knows their locations? Because the Master Emerald was where Tikal stayed with Chaos for the past 4,000 years, so in essence, it's her home.
In Tails'/Big's story, when Big tries to get Froggy back from Tails, you can see (despite the bad graphics) that Big's eyes glow in the dark. This is similar to real life cats that reflect light in their eyes when it's dark.
Knuckles stops giving a crap about protecting the Master Emerald after this game, barring finding the pieces in Sonic Adventure 2, and why would he? His people likely started the entire millennia-long tradition of protecting the Master Emerald solely to keep Chaos sealed within it, and as Knuckles says, even he doesn't know exactly why he's doing it at this point. With Chaos both free and no longer actively genocidal after this game, Knuckles' life's mission of protecting the Master Emerald is now effectively moot and he can carry the Master Emerald around wherever he goes anyway, so he can now do whatever he wants.
Additionally, since his introduction, Knuckles has seen the threats escalate, from just his island to the entire world. He's figured out that it doesn't matter if the Master Emerald is protected if the world gets destroyed in the process.
The title of Knuckles' theme, "Unknown from M.E.", seems weird, until you realize that "M.E." is an abbreviation of "Master Emerald".
The beginning of Crazy Robo, E-101 MK. II's boss theme, sounds like a Dark Reprise of Gamma's theme, before turning into a different composition. This can be seen as symbolic of Beta himself. He starts out being near identical to Gamma, outside of a darker paint job, but is then turned into a very different machine to what Gamma is.
Sonic's Sky Deck has a sequence where the Egg Carrier makes sudden and dramatic tilts. Knuckles' Sky Deck — which takes place at roughly the same time — has a gimmick of using a lever to tilt the Egg Carrier to access certain places. Do the math.
ZERO is in fact officially termed E-100 Alpha ZERO in certain bios. It continues chasing and antagonizing Amy and Birdie, even long after Eggman has stolen the latter's Chaos Emerald. ZERO lacks an animal battery, a "soul" in some sense. Capturing Birdie and consuming it would have made him akin to his younger brethren.
As noted above, E-101 through to E-105 all have birds as their animal batteries, which would explain why ZERO doesnt try to pursue another animal. Hes specifically trying to be as similar to his brothers as he possibly can.
Perfect Chaos' path of destruction suddenly starts to seem extremely bad if you consider how many innocent people must have died. He creates a tidal wave that completely floods the entire city, causes water to rip through and destroy buildings, and basically causes a path of havoc similar to that of a extremely disastrous tsunami. I mean, JUST LOOK at how destroyed the city is in a matter of only minutes...at the very least, the people in the building would all die or be SERIOUSLY injured. Again, JUST LOOK at the cut-scene where the water rips through the buildings. ...Don't forget this was a game primarily aimed at kids. Not to mention that after a certain and rather recent real life tragedy...this has become a major source of Fridge Horror.
They didn't disappear. The cutscene with Sonic going Super takes place after Chaos is done destroying Station Square. So most inhabitants are likely dead by that point, their bodies lying below the water and ruins.
In the final story, Tikal insists that the only way to stop Chaos is to seal him into the Master Emerald again. Given the last time she did this required her to sacrifice her eternal soul into the emerald along with him, the implication is that she either intends to do this again (albeit with permanent intention) or, if her lack of physical form prevents her, sacrifice someone else.
Note that she says to Sonic "We have to seal Chaos in the Master Emerald!". Not I, we. It's very possible that she was trying to ask Sonic to sacrifice himself since she couldn't, but before she could go into detail, their conversation was interrupted when Sonic's friends arrived with an alternate, superior solution.
Consider this lyric from Sonic's theme: "It doesn't matter who is wrong and who is right". Does he rush into battles with no consideration of ethics?
Casinopolis has some horror in it. The Chaos Emerald in the stage is located in a vault that has a moat to protect said emerald. The large arms, presumably to allow the user to handle the emerald, operate via a button. The button that activates the arms is in essence a security device. If you have no official access to the emerald, the arms shake you violently as a means to make a point to stay away. So how does Sonic go around this system? Why, basically collecting enough rings to fill in the moat every time the machine tries to punish Sonic. In essence, Sonic is conducting a heist by voluntarily hurting himself.
Casino-themed levels in Sonic games are nothing new. You may have noticed they always seem to focus exclusively on the fun side of going to the casino, never the dark side of gambling. Landing on Eggman and losing rings is always a pain, sure, but that's nothing compared to the horrors of real-life gambling addiction. Rule of Fun though, right? Do you really expect them to make a Sonic game where bad luck at gambling means being thrown out of your bright, fun life, forced to get the rings you desperately need in much more dangerous ways, all while living in ruin among heaps of garbage and............huh, yeah, they totally did go there. Right. Guess Casinopolis is realistic for a Sonic game in more ways than just looking mostly like a real casino.
Pretty sure that the mechanical arms shake you to "extract" your collected rings you and deposit them in that "ring vault". Note that they put a ring counter on it. The Chaos Emerald was likely placed there as an incentive and reward for depositing enough rings. Ergo, Sonic didn't steal anything.