NeoSpeedFreak
Trainer
I don't know how to script, but here's my idea:
You moved in Johto one day later that Ethan, Lyra and Silver obtained their starters (Cyndaquil, Chikorita and Totodile respectively), because Elm doesn't have more starters, you have to choose between Bagon, Gible and Deino; you will the Johto Sarters from eggs obtained by their respective trainers after beating them the first time, the 4 will ally to defeat Team Rocket, because their plan is creating ''Mewthree''/New Mewtwo Form (let's call it M3 for brevity), and Giovanni would use it to conquer Johto, Kanto and beyond.
The 4 will try to ally the Kanto and Johto Leaders (some will be harder to ally, or they won't ally), after getting the 8 Johto badges, Ethan, Lyra and Silver will capture Ho-Oh, Celebi and Lugia respectively; (The Dogs will be captured like in HG/SS). But YOU WILL CAPTURE XERNEAS (HS) OR YVELTAL (VG)! (After getting all the Johto legendaries and the respective new legendary you can capture the other new legendary).
Of course, after beating the league once, Kanto awaits you with the other 8 badges, the final battle against Team Rocket, Suicune, ALL the other region starters, Bill with a Sylveon, Red and Green (A.K.A Leaf).
You will get M3/Item to change Mewtwo into M3 from Giovanni after you defeat Green/Leaf, and Ho-Oh, Lugia and Celebi are released by their respective trainers after you defeat Red, and they are captured in their respective places in G/S/C, GS Ball is obtained from Kurt after beating Red.
You moved in Johto one day later that Ethan, Lyra and Silver obtained their starters (Cyndaquil, Chikorita and Totodile respectively), because Elm doesn't have more starters, you have to choose between Bagon, Gible and Deino; you will the Johto Sarters from eggs obtained by their respective trainers after beating them the first time, the 4 will ally to defeat Team Rocket, because their plan is creating ''Mewthree''/New Mewtwo Form (let's call it M3 for brevity), and Giovanni would use it to conquer Johto, Kanto and beyond.
The 4 will try to ally the Kanto and Johto Leaders (some will be harder to ally, or they won't ally), after getting the 8 Johto badges, Ethan, Lyra and Silver will capture Ho-Oh, Celebi and Lugia respectively; (The Dogs will be captured like in HG/SS). But YOU WILL CAPTURE XERNEAS (HS) OR YVELTAL (VG)! (After getting all the Johto legendaries and the respective new legendary you can capture the other new legendary).
Of course, after beating the league once, Kanto awaits you with the other 8 badges, the final battle against Team Rocket, Suicune, ALL the other region starters, Bill with a Sylveon, Red and Green (A.K.A Leaf).
You will get M3/Item to change Mewtwo into M3 from Giovanni after you defeat Green/Leaf, and Ho-Oh, Lugia and Celebi are released by their respective trainers after you defeat Red, and they are captured in their respective places in G/S/C, GS Ball is obtained from Kurt after beating Red.