And who better to take down a proverbial Physical God hyped up on so much raw power as well as all seven Chaos Emeralds than Sonic? He had personally helped train Emerl and get the Gizoid started off in the first place, watched over Emerl's progress throughout the entire game and seen both his advantages and flaws as he copied techniques from all of his friends and himself, and knew Emerl was in his own suicidal equivalent of a Super Form. Sonic knows his friend's moves thoroughly (as should the player by this point) and is the most experienced fighter in the entire cast with the Emeralds, arguably even dwarfing Knuckles' knowledge on how to counteract them and Shadow's reliance on Chaos powers. Sonic didn't simply fight Emerl because he's the titular protagonist and obligated to it - he's singlehandedly the only absolute counter to such a foe thanks to having more experience than even Shadow, and the story proves it by having him waste Emerl without even seemingly breaking a sweat in under 30 seconds with no Emerald assistance of his own. And Sonic manages to do this despite Emerl's moves being amped-up versions of his own.
All of the final boss' moves are effectively enhanced versions of Sonic's moveset, with more damage, faster execution and additional effects (such as punches causing explosions, kicks sending out twisters). This final boss happens to house all of the Chaos Emeralds. In essence, you're fighting an equivalent of Super Sonic.
At first, Chaos appearing as an optional battle at the last story seems like a case of Giant Space Flea from Nowhere but actually makes sense. Chaos is a total foil to Emerl;
Both Chaos and Emerl are 4000 year old highly destructive beings who are responsible for the destruction of an ancient civilization. Both of them also can absorb Chaos Emeralds to grow in strength.
Chaos is an organic, watery being who was peaceful by nature and driven to violence. Emerl is a robotic being whose violent by nature but was given the ability to be peaceful.
Chaos's powers comes from mutations and utilizing water and air spirits to aid in combat, whilst Emerl's power comes from super science.
Both of them were studied by Professor Gerald; Emerl directly, and Chaos through the artificial Chaos (and possibly through Chaos Drives) They were also both rediscovered by Eggman.
Finally, Both of them revert to their original natures, making them an example of Nature vs. Nurture. Chaos reverts to his peaceful nature and lives in relative peace...but unfortunately, Emerl reverts to his violent nature and is subject to Shoot the Dog.
