Yeah, unless we count Sonic Spinball,
but Freedom Fighters are just cameo in there.
https://www.youtube.com/watch?v=Z8P-l5TDimw
No I mean, SatAM and Archie comics had Dr. Robotnik (later Eggman) took over Mobotropolis with his legion of SWATbots and roboticized the denizens to contribute to his work force in creating more SWATbots and other weaponized machines for warfare. The survivors of Mobotropolis banded together and with other mobians from other places formed a counter-faction against Robotropolis. So in a sense it was a civil war of sorts against the Freedom Fighters and Robotropolis which overtime Dr. Eggman upgraded it into an empire.
Sonic Forces sort of had that. Dr. Eggman started a war and conquered the world and you're part of a band of freedom fighters to resist against Dr. Eggman.
I bet Frontiers won't even mention it. That the fact he conquered 99% of the world is just swept under the rug.