>>54503517Start the player in Kanto, have the game be 1:1 with RB until you get to the S.S. Anne, which gets attacked by Team Rocket. The ship crashes and the player ends up in Cherrygrove, where the journey continues just like the original Johto but with higher levels and more Johto Pokémon appearing.
Team Rocket plot is rewritten. Giovanni appears on the S.S. Anne and vanishes after the crash, assumed dead. TR grunts delude themselves into thinking he's just in solo training and try to get his attention through crime, but the Executives know the truth. Their actual plan is to hijack the airwaves to control Lugia (to find Giovanni's body at the bottom of the sea) and Ho-Oh (to resurrect him). The legendaries don't actually appear in the story though because you foil the plan before they can fully execute it. In the post-game, you find him in Tohjo Falls and learn it was actually the grunts that were right all along.