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.
Another small but interesting difference can be seen when Sonic and Amy meet at Station Square. In Amy’s version Sonic runs away from her and she must catch up to him at Twinkle Park. In Sonic’s version Amy insists that she’s coming with him and she’s walking next to him when they get near Twinkle Park. It’s a nice reflection of how Amy sees Sonic as being distant and impatient while Sonic views her as being pushy and clingy.
Tails’ level design and story events revolve around his insecurities. When Sonic is around, Tails’ version of events has him tackling all the boss fights, and his levels are about him racing and beating Sonic to the end of the levels. This can be seen as Tails fantasizing about being the cool, confident one out of the two. Whenever Sonic isn’t around, Tails spends this time lamenting about how much he relies on Sonic. Things come to a climax when Tails has to race Eggman to deactivate a missile and then fight him alone. Given the Self-Serving Memory nature of the games events, this last encounter against Eggman may be the only one that is objectively true within Tails’ story.
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.
There's also the fact that green eyes are often associated with the wind element, just like Sonic, who's often described as being as "free as the wind", has had many wind-based attacks such as Sonic Wind, and was given the "Knight of the Wind" title in Sonic and the Black Knight.
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 dated 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".
In one of the lyrics, Knuckles claims that "I was born by myself", which seems pretty nonsensical. That is until you remember that echidnas are monotremes, mammals who lay eggs rather than giving birth. And considering that he's Last of His Kind, there's a more than zero chance that Knuckles quite literally was born, or rather hatched, by himself.
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 doesn’t try to pursue another animal. He’s specifically trying to be as similar to his brothers as he possibly can.
Having Gamma be required to shoot Eggman's artillery to keep his life timer seems like a non-sensical approach at first, but it is pretty much in-character for the both of them. Eggman making his robots dependent on blasting everything on sight and causing destruction seems ideal at first, until keeping in mind he has dispatched his badniks all across the globe and Gamma, being an impersonal droid with no evil will of his own, just blasts them indiscriminately. One of the first establishing cases that both Eggman Didn't Think This Through and Gamma is Just Following Orders.
Big's gameplay seems odd and hard, until you realize it's like actual fishing. And how do you catch fish? Take it slow and easy, like Big does. Tire the fish out. Slowly, but constantly, reel them in.
Amy's theme song "My Sweet Passion" has Amy express that Sonic "reminds her of parsley when he's standing there alone". As random as this might sound to most listeners, it makes sense in the respect that parsley is never eaten alone but rather used to season meals. This highlights how Amy doesn't just love Sonic, but views her and him as being explicitly incomplete without the other.
Chaos being the first known guardian of the Chaos Emeralds (and very likely the first period, given that he's descended from the ones who brought them to Earth in the first place) explains why their names are so similar - the natives likely named the emeralds after the one who held them.
Eggman knowing when Gamma has collected his Jet Booster but not when he freed Amy may seem like a plot hole... but then you remember this is Eggman we're talking about. It's likely Eggman was aware of Gamma's treachery but didn't have time to punish him for disloyalty with Sonic and Tails closing in. So telling Gamma to collect the Jet Booster and head to the deck was a combination of a Uriah Gambit and a Xanatos Gambit. If Gamma manages to beat Sonic & Tails, then he's gotten rid of the two biggest thorns in his side; if Gamma loses, then that saves Eggman the time of needing to scrap or reprogram a faulty robot. Either way, Eggman wins.
Tails opting to paint his Tornado II (and his Cyclone in the sequel) blue with yellow sections makes perfect sense. The guy he idolizes is blue, and can transform into a yellow form.
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.
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?
Perhaps Sonic listens to his heart regarding what is morally just. He doesn't totally eschew other peoples' input — if he did, Gamma wouldn't have been spared after their fight — but he does a pretty good job taking his own judgment on things into account. In other words: "It doesn't matter who is wrong or who is right; I'm doing what I know is right."
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.
When Sonic and Tails board the Egg Carrier, Eggman sends Gamma after them. Though the boss isn't much of a hassle at all gameplay wise, the cutscenes and Gamma's interpretation imply he was quite a challenge for Sonic. Consider the heroes' chances if Eggman hadn't committed the huge Villain Ball of demoting his other E-100 models beforehand, leaving four of them to deal with (and the other three likely without the same conscience for Amy to break through).
Chaos turning on Eggman seems like a standard The Starscream moment many of the doctor's cohorts would commit to in future games, until you keep in mind that the last occasion he was with Eggman, he abandoned Chaos on the falling Egg Carrier. Given Eggman was the one companion he had in a very long time, being left for dead must have been pretty damn sore. Chaos didn't turn on him just for failing to help his ends, he turned on him because he couldn't trust him anymore.
