Curate, connect, and discover
(finally found this again yay!!)
To add on: I had a thought a while back after seeing this post for the first time, that the world where Maria survives could be the New Yoke one? And perhaps Dr. Done-it could be Gerald.
I don't know my Sonic lore too well yet as I'm pretty new to this fandom but maybe Gerald figured out a way to cure Maria at the cost of Shadow? GUN could've been pissed about loosing the ultimate lifeform and had the project shut down. Or not at the cost of Shadow, but that GUN simply wouldn't like how Shadow was used for medicine and healing instead of training to be a weapon and still send that squad to get Gerald & Shadow. However instead of Maria getting shot it would be Shadow? He could maybe be weakened and vulnerable somehow as a result of finding the cure for Maria and his immortality and healing aren't working because of it and dies. However I'm not so sure what could lead to Gerald becoming evil, but one way or another it happens and Maria (going by the vibe I've gotten from the movie and what I've seen of the project shadow lore) would be opposed to him. She could be aiding the rebellion in New Yoke, working from the shadows to bring the Chaos Council down. She'd most definitely be aged up but by how much, I'm not sure. With this I personally see seasons 1 & 2 being largely the same outside of Rebel & Knuck mentioning an unknown helper (maybe they call her Shadow and Sonic thinks it's a version of Shadow and doesn't realise it untill season 3?).
Season 3 would then need a rewrite to include more of Shadow and explore the Maria & Shadow dynamic, especially with the versions of them who've lost the other. During episodes 3x1 and 3x2, Shadow could remove the inhibitor rings to get a power boost, get out of Grim and start figuring out where Sonic is. Meanwhile in New Yoke, Maria could reveal herself and help get the citizens safely to the Chaos Council base (maybe appealing to Gerald to let them in?). Shadow could then appear and cue angst!
Not sure how to continue it from there so someone much more talented and knowledgeable of the lore and characters can take it from there :').
Artist Credit for Maria: @blazy-art