Well... onto Johto. GS ball is still into play. Tracey joins them until Kurt.
Ash
- Leaves all his Pokemon (Except Pikachu), behind at the lab.
- Heracross remains his first capture
- Bayleef is still a thing and the gag also stays
- Instead of in Sinnoh, i am evolving Cyndaquil here into Quilava
- Totodile evolves as well, into Croconaw
- GS ball plotline with Celebi and Giovanni
- Ash gets a Heavy, Lure, Fast, Level Ball from Kurt
- Ash meets his Johto rival after this, Silver (Silver has the following Pokemon: Sneasel, Murkrow, Ursaring, Houndoom, Ampharos and Hitmontop and all of his Pokemon have a rivalry with Ash's Johto ones).
- Shiny Hoothoot capture in Ilex Forest, using Pikachu, then evolution into Noctowl against Morty. Hoothoot is caught in a Level Ball
- Pokemon Race against Gary and Silver. Team Rocket interferes with the race. Ash wins. Gets a Pokemon Egg
- The Egg hatches into a Larvitar, who later evolves into Pupitar after battle with Silver.
- Ash loses twice against Clair with his Johto mons, so he decides to call upon some older friends. Lapras defeats Kingdra, who in turn gets defeated by Gyarados. Pikachu in turn ohko Gyarados, the weakest link in Clairs team. This leaves Dragonite, who defeats Pikachu, sustaining heavy damage. Venusaur comes in to seal the deal for Ash.
- Pokemon League happens. Ash vs Silver is a six vs six, so is Ash vs Gary. Ash battles Silver with Pikachu vs Ampahros, Noctowl vs Murkrow, Heracross vs Hitmontop, Ursaring vs Bayleef, Quilava vs Houndoom and Croconaw vs Sneasel. Ash wins. Gary is next, which Ash calls upon his reserves, to fight alongside Pupitar. Ash wins as well, only to lose to Harrisson and learning about Hoenn in the next round.
Brock
- Gets a Pinsir in the same episode as Ash gets Heracross (Which has consequences for Foretress)
- Charmeleon evolves into Charizard during the GS ball plotline
- Gets Heav and Fast ball from Kurt
- Brock enters the heavy Pokemon contest with Graveler. Graveler evolves into Golem, granting Brock the win (Slight deviation from the main anime, but i found it fitting for Graveler to evolve here and this is way i didn't evolve it in Kanto, which was my original plan).
- Leaves Charizard behind in the Valley.
- Catches a Magcargo
Misty
- Has left all her Pokemon at the gym, except for Poliwhirl and Starmie
- A stray Wooper joins her team in Violet City, which evolves at the Whirl Islands
- Togepi evolves into Togetic protecting Misty from Team Rocket during the GS ball plot
- Poliwhirl evolves into Politoed during the Rage of Lake events
- leaves after Johto to become a full time Gym Leader
Tracey
- His Scyther evolves into Scizor
- Leaves after the GS ball plot to help at Oaks ranch.
You might think i made a few weird decisions, especially since aside from Noctowl, Ash hasn't gotten any Fully Evolved Johto mons, which is done on purpose, as to him still being a relative newbie, having only one other region under his belt. I also made the change to evolve Cyndaquil and Croconaw, due to Ash missing out on Charizard and Squirtle in Kanto. Him not getting Phanpy (Despite his Donphan being one of my favorite mons and it being one of my favorite mons in general), it didn't really fit with what i have planned for the future, so thats why i gave him Pupitar instead.