>>714518645The games have always been a kinda "Chaos vs Order" story, with Sonic representing good chaos (freedom and possibility) and Eggman representing bad order (restriction and tyranny). Chaos himself is naturally the negative force of chaos, wild and uncontrollable, even to himself, becoming trapped by his limitless power and unable to direct it to any goal beyond broad feelings.
Fighting Perfect Chaos is more about the end of Sonic's story rather than the overall plot, as it's a bunch of small character-driven stories woven together. Sonic's story is mostly a collection of events from the past games (Tails getting his plane shot down only to come back in the nick of time, a misunderstanding with Knuckles, rescuing Amy from an Eggman robot, etc), so the epilogue allows Sonic to do something more than just beat up Eggman and inspire others. He gets to directly confront Chaos with the full knowledge of his past now, and wants to find a way to move forward from it instead of simply sealing him away. Super Sonic is everyone's wish for a future beyond the ruins that Chaos has wrought, with Sonic being the light towards that future.
Chaos became enraged at past misdeeds and became trapped by those feelings, becoming stagnant and more destructive than the people who wronged him. Sonic witnessed the entire city he spent all game protecting still get destroyed, but he didn't give up despite that, always focused on the way forward, even for Chaos himself. Knuckles might be the one closest to Chaos lore-wise, but Sonic is his thematic opposition, so that's why they get the big confrontation by the end. Sonic inspires everyone he meets to live their lives to the fullest and open their hearts, being able to take in all the small stories he's helped influence and combat the embodiment of a closed-off, all-destroying monster. It's all just playing off of broad themes the series uses, rather than a specific theme towards Adventure 1 itself.