Remember how LGPE was accurately leaked weeks before it was officially announced? I remember we had so many rumors about new game taking place in Kanto (reboot/remake, no one knew).
I wasn't a fan of the idea, but taking the RR endgame of Ultra into account, I kept playing with the idea of the mystery Kanto game focusing on you being from the Kanto Giovanni took over, since the "worlds where the villains won" idea had a lot of potential, and I think Giovanni's plans would have been the easiest to work with and form a what-could-happen-after scenario with.
The idea was you happen to break TR/RR's enforced curfew one night tho Blue (searching for his missing grandfather) bails you out and gives you your starter (which he bred from his own, tho you find that out later.)
He's the new leader of a Rebellion comprised of Misty, Brock, Erika, and various civilians around the region, which you also join. (Later major additions are Blaine, who had stepped down from his role as a Gym Leader due to his shame at having been a TR/RR scientist/role in the creation of Mewtwo, and Janine, who is frustrated at her father for allowing TR/RR to occupy their city and acting as muscle for them.) Your goal in the story would be to liberate Kanto's cities from TR/RR, which would have fallen under the control of the HGSS admins, Sabrina (implied to have a thing for Giovanni), Surge (signed on since Gym battles didn't thrill him anymore), and Koga (wanted to protect his daughter), as they were initially villains in the manga, and I always loved the idea of more villainous Gym Leaders aside from just Giovanni.
I kind of imagine the roster being:
Viridian City: Archer, is still fought last
Vermilion: Surge (he's taken to working off the SS Anne rather than his Gym)
Fuchsia: Koga, where Janine joins up you after saving you from him (He later abandons TR altogether when Janine leaves to go fight them with you, realizing how much of a coward he was, tho it's some time later you learn this.) More on the saving thing, you are captured and dragged into his Gym by some more Elite members (I imagine a middle spot between the regular grunts and the Executives, kinda like we get with Flare's admins), and he is forced to use Poison Gas on you in order to get rid of you, and that's where Janine comes in, using her Ariados to restrain everyone and drag you out of danger.
Cinnabar: Blaine, tho he's stepped down in shame over his role in Mewtwo's creation
Saffron: Sabrina, tho she operates out of Silph Co.
Fought more like Proton > Petrel > Surge > Koga (Janine steals his badge and gives it to you) > Ariana (Celadon being one of the biggest holdouts) > Sabrina (Saffron being the actual biggest one, this would also be where Koga joins you) > Archer. Blaine doesn't have a proper Gym Battle, but he gives you a badge when you help him free the Legendary Birds from TR's control, which would happen between Ariana's and Sabrina's battles.
The Sevii Islands would have played a role as TR's last holdout once they're chased off the mainland, and the E4 members are being held there with the exception of Lorelei, who had managed to escape (popsicled Petrel and some grunts, who had been sent to capture her), and who you'd assist in rescuing the other League members.
This would be around the time where RR's Giovanni would return for one final boss battle against Team Rocket, his defeat finally fully liberating the region. (You then go fight the reinstated E4 and are crowned Champion, with Blue giving you your first battle as Champ a la Kukui, and is proud of you for how far you've come as a trainer.)
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