Sonic the Hedgehog 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:
Contents
The Intro Sequence
According to most sources, the opening sequence of Sonic 3 with Super Sonic takes place only moments after the ending sequence of Sonic the Hedgehog 2, following Sonic's plummet from the Death Egg. (Just don't ask where the Tornado suddenly got its rocket booster from, or how Robotnik managed to build Carnival Night and Launch Base Zone so quickly!). 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.
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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 enabling 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. In both of these sequences, Sonic loses the Master Emerald in the stratosphere and the Floating Island does not reascend. If Sonic has incomplete heptets of either the Chaos Emeralds or Super Emeralds, the final fade-to-black shows Robotnik chuckling beside the Master. However, if Sonic still has exactly seven Chaos Emeralds (either by collecting them when playing Sonic and Knuckles on its own, or by never going into a Giant Ring and the Emerald Shrine in a docked S3&K), instead 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).
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Conflicting Evidence
However, not everything is nice and consistent. 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 did not get the Master Emerald back (rather it ends up floating around in the sky somewhere), and Angel Island is still sat in the sea. This despite the fact that the ocean background in Knuckles' Angel Island Zone is replaced with sky compared to Sonic's, and that the island is clearly up in the air during Knuckles' last boss, Super Mecha Sonic. Another oddity is 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.
In Conclusion
While there are some inconsistencies however you look at it, (articularly regarding which of Sonic's endings leads into Knuckles' game; it seems a reasonably save 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 Hyper Knuckles ending).