I'm developing my own vision of this rumored concept on my DeviantArt and it has like... 6 phases? Well, technically not at all due to a crossover it haves. It has some weird ideas on his story, but it's still a very solid foundation.

While I was developing it (I'm in the final saga), I decided to ask you how you would do it. How many phases would it have? Would it follow a structure similar to that of the MCU or a more independent one? Which arcs would be the main ones?

In the case of don't be sure, here's how I would structure to it to, maybe, give you an idea:

Phase 1: Presenting each Freedom Fighters members and the most iconic heroes and villains. (Main antagonists: Eggman, Metal Sonic)
Phase 2: Develope the echidna society lore. Introducing series and very subtle references to other realities. (Main antagonist: Chaos)
Phase 3: The space and alien invasions, developing better the Shadow origin. Projects set in other universes starts to appear. (Main antagonists: Metarex, Black Arms)
Phase 4: Multiverse in his maximum expression, the "Endgame" of the original Freedom Fighters team. Introducing elements like the Zone Cops, the Metal Virus or the anti-universes. (Main antagonists: Scourge, Ix, Eggman, Dr. Starline, Surge)
Phase 5: Based on Mobius: X Years Later, showing the rise of the new generation, what happened to the old heroes and the new threats. (Main antagonists: An Eggman 2nd or something like)
Phase 6: The Super Genesis Wave, ending with a Secret Wars-like crossover and the reboot of the reality. (Main antagonists: Eggman 2nd, Time Eater and maybe a cosmic entity and maybe other cosmic entity, in the case of exclude Mega Man)

I mixed elements from various media, especially games and comics. It isn't necessary to follow the structure of the real life productions, you can follow the one you consider best. Also, both MCU-like structures and more independent ones are accepted.