Sonic 3 & Knuckles chronology and endings
From Sonic Retro
In Sonic 3, Sonic & Knuckles, and the combined Sonic 3 & Knuckles, the chronology of Sonic & Tails' story compared with Knuckles' is never spelled out explicitly. Does Knuckles' story, and his fight against Eggrobo, occur before, during, or after his confrontations with Sonic? How are the two routes through the game connected together?
While there is no single point in Sonic 3 & Knuckles that can be cited as definitive evidence of how and when the stories are linked, the game provides clues here and there which add up to a reasonable case. Let's review the evidence:
The Intro Sequence
The opening sequence of Sonic 3 takes place "many days" after the ending of Sonic the Hedgehog 2 and Sonic's plummet from the Death Egg - not immediately succeeding it (note the lack of a booster on the plane in the ending of Sonic 2). As Sonic and Tails go to investigate mysterious happenings out to sea in the Tornado, Sonic transforms into Super Sonic, jumps off the plane and tears over the ocean, onto the beach of Angel Island, which has been pushed out of the sky by the weight of the crashed Death Egg. Knuckles punches out Sonic's Chaos Emeralds and the gameplay begins.
According to the character played and the number of Chaos Emeralds and Super Emeralds collected, different endings can be triggered. Once the game is completed, the Level Icon for that save slot will change to a Character Icon, as seen in this table.
Hyper Sonic Ending
In the "best" ending of Sonic's story, after beating Doomsday Zone with all the Super Emeralds, Hyper Sonic shepherds the Master Emerald back down through the atmosphere, where he and the gem are picked up by Tails in the Tornado. They fly past Angel Island, dropping the gem off and enable the island to rise back into the sky as Knuckles looks on happily.
Alternative Sonic Endings
However, if Sonic has not collected all the Super Emeralds, one of two possible alternate endings play, depending on his Chaos Emerald count. If Sonic has not collected all of the Chaos Emeralds, the game ends after the Great Eggman Robo and chase scene in Death Egg Zone. Sonic loses the Master Emerald while falling through the stratosphere, and the final fade-to-black shows Robotnik chuckling beside the Master Emerald.
On the other hand, if Sonic has all seven Chaos Emeralds, but not all of the Super Emeralds, then he enters Doomsday Zone as Super Sonic, eventually returning the Master Emerald to Angel Island as in the Hyper Sonic ending. Now the final sequence shows an Eggrobo rising out of a pile of wreckage (of other Eggrobos). The implication seems to be that this is the robot which goes on to fight Knuckles in the echidna's playthrough.
Knuckles After Sonic?
If Knuckles' Eggrobo opponent only rises up after Sonic's end sequence, this indicates Knuckles' playthrough might take place after Sonic's. There are a few other tidbits in the game which indicate this to be the case, as we see below. In Sandopolis Zone Act 2, the Hyudoro ghosts are accidentally freed from an Egg Capsule during Sonic's playthrough; when Knuckles gets to the same point, the pod is already cracked open. Combine this with the Death Egg's absence in the roof of either Lava Reef or Hidden Palace Zone, and it seems that Knuckles' playthrough must occur at least after the battlestation launched (witnessed in Sonic's Sky Sanctuary Zone). More circumstantial evidence lies in the fact that the fight between Sonic and Mecha Sonic, combined with the disruption of the passing Death Egg, seemed to destroy much of Sky Sanctuary. When Knuckles arrives, his level is conspicuously smaller, the implication being that this is the only piece of the floating ruins left. Interestingly, the Death Egg's appearance in Lava Reef's first act is considerably less noticable than in its second act, as noted in the gallery below.
If we infer from the points above that Knuckles' story takes place after Sonic's "middle" ending - where the hedgehog had the seven Chaos Emeralds in the Doomsday Zone, leading to the Eggrobo wreckage scene - then at the end of Sonic's story Knuckles got the Master Emerald back, and Angel Island began to rise out of the sea. Indeed, we see that the island is clearly up in the air during Knuckles' last boss, Super Mecha Sonic. Even in the Sonic 3 parts of Knuckles' playthrough there are signs that Sonic's Sonic & Knuckles story has concluded; the ocean background from Sonic' Angel Island Zone is replaced with sky when playing as Knuckles, and the crashed Death Egg is gone from the Launch Base Zone Act 1 backdrop. Lastly, in Knuckles's Mushroom Hill Act 1, the entrance to the corridor that Knuckles closes in Sonic's story is open, indicating that someone was inside.
An oddity is that Angel Island is not burned and charred until the Fire Breath encounter for both Sonic and Knuckles. However, there is no evidence that Knuckles' story takes place directly after Sonic's, and thus some time could have passed and the shrubbery could have regrown since Sonic's time on the Island. One thing to also note, however, is that at the end of Sonic's story, when we see Knuckles standing with the Master Emerald looking out at Sonic, the dreadlocked hero is standing in a jungle area seemingly identical to the once charred Angel Island Zone. It is possible, however, that Knuckles is simply in an area that wasn't burned...
Another difference is in Sonic's story, Sonic defeats Mecha Sonic, but the robot does not explode—he merely looks shorted. Mecha later fights Knuckles, and after Knuckles beats him, THEN he explodes (provided you have collected 7 Chaos Emeralds).
A small oddity might be the presence of the Flying Battery in Knuckles' playthrough (with Robotnik instead of Eggrobo as a boss, to confuse matters further), despite the fact that the airship was seemingly damaged or destroyed in Sonic's story. The game staff have indicated that Robotnik's presence here is simply due to the fact that there was no available sprite for Eggrobo in the Hang Mobile's cockpit.
As it seems, Flying Battery was originally to be placed between Sonic 3's Carnival Night and IceCap. As Knuckles uses a teleporter to go directly from the former to the latter, it is possible that in the original game plans Knuckles was not to have gone through Flying Battery at all. This would explain the lack of alternate routes made specially for Knuckles, and why there is no Eggrobo cockpit sprite: The developers at the time did not make one as Knuckles would not have fought that boss. Once the game was split, Flying Battery was added to prevent Knuckles's story in Sonic & Knuckles from being unusually short; if Flying Battery is excluded, Sonic & Knuckles alone only sees Knuckles going through Mushroom Hill, Sandopolis, Lava Reef (with no boss), Hidden Palace (which is just a pass through to the next zone), to the final encounter on the remaining land of Sky Sanctuary, essentially 3 full zones compared to Sonic's 6.A bug also sometimes sees Knuckles fight Robotnik in Mushroom Hill Zone.
Continuity and character interaction
Another way to prove Knuckles' game takes place after Sonic's is by observing the appearances of one character during another character's gameplay, the strongest piece of evidence remaining Knuckles' ending, where Sonic saves Knuckles after Sky Sanctuary Zone collapses.
Of course, it can be pointed out that by that point of the game, even during Sonic's playthrough, all the differences between Sonic and Knuckles have been resolved, after Sonic and Knuckles fought in the Hidden Palace, and witnessed Robotnik stealing the Master Emerald. The problem is: that fight never occurred in Knuckles' version of Hidden Palace Zone. In fact, except for the ending, Sonic does not appear in his game at all, while Knuckles makes eleven appearances during Sonic's game, not counting the ending. During six of which Knuckles is seen in places where he's unable to go during his playthrough, mostly in Sonic-only parts of the following acts: twice in Carnival Night Zone act 2, once in each of Launch Base Zone acts, and the only act in Hidden Palace Zone, from which he follows Sonic to the Sonic-exclusive version of Sky Sanctuary Zone (counting both as a single appearance)... oh, and the high ledge after the Angel Island Zone boss fight which is only visible during cutscenes.
If these adventures were in fact supposed to be taking place at the same time, Sonic's encounters with Knuckles during Sonic's story would arise a lot of continuity issues, as he would seem to appear in two places at once. Alternate routes through several levels, where Knuckles does not even come close to the places where Sonic meets him during his game (not to mention his completely different versions of Hidden Palace Zone and Sky Sanctuary Zone) disprove any attempt at interpreting the absence of cutscenes featuring Sonic during Knuckles' game as a case of gameplay and story segregation. It is the same thing for Sonic's cameo during Knuckles' ending: if he is flying the Tornado and saving Knuckles after Sky Sanctuary collapses, who is storming the Death Egg (and, by the way, where is it) ? Thus, the only way they could possibly make sense is if the two playthroughs were at least not happening at the same time.
Now, we are left with two possibilities: either Sonic's story happens before Knuckles' story, or vice versa.
Let's look at Knuckles' ending again. It appears, from the fact that Sonic obviously thinks enough of Knuckles to come to his rescue, and that Knuckles never runs into Sonic during his story, that Sonic and Knuckles reconciled before the latter's adventure started. On the other hand, Sonic is antagonistic with Knuckles at the beginning of his (Sonic's) story, and allies with him towards the end. Let's assume that Knuckles' playthrough happens before Sonic's. This way to tie the two stories is inconsistent for two reasons: first of all, it does not make sense for Sonic at this point to be friends with Knuckles (or even to know who he is), much less save him. And finally, during Sonic's story (which would follow this ending chronologically) , it makes no sense for Knuckles to be antagonistic towards someone who saved his life (but then, who knows how convincing Robotnik can be?). Bottom line, this approach is not satisfactory.
Thus, the only logical way of tying the two adventures together is considering that Knuckles' adventure happens after Sonic's.
It seems a reasonably safe conclusion, especially given the Lava Reef / Hidden Palace space station absences, that Knuckles' adventure occurs after Sonic and Tails have flown away from the island (although Sonic briefly returns with the Tornado to catch Knuckles in the ending).