Pt two of the gen 1 stuff (pt1 here) this will expand on plot
Kanto is broken up into A-Plot and B-Plot (A-Plot being regular Kanto adventures with Ash Gary Misty and Brock, B-Plot begins to appear around Vermillion with actual Team Rocket substance)
Jessie and James use trying to steal Pikachu as a cover for their actual mission being passing along information to Brock
Celadon is the true kickoff point of B-Plot, annual Celadon Flower Festival starts and Brock conveniently has to spend more time with Erika since he is having flare ups again (unique chronic illness that sadly the majority of the surviving population of Orre had fallen victim to, Brock had contracted it as an infant) she has been working for years on synthesising a proper medication and possible cure (Erika is pretty much the reason why Brock isn't permenantly bedridden and is able to travel again post having to drop out of the league circut back when he was Leaf's rival)
Lance makes appearances throughout 1st being Flower Festival being a Good ChampionTM (que Ash fanboying getting to meet his idol in person, Gary and Misty tease Ash and they both mention that he should go see Erika since she would be happy to see him, Erika does NOT want to see Lance right now of all times)
Flash ahead to Saffron Silph Co takeover (Brock had left right before arriving to Saffron bringing up something urgent back in Pewter, Sabrina is nowhere to be seen during said takeover and every Rocket Grunt seems to only be targeting Indigo League Enforcement while ignoring civillians) Ash decides now is the best time to prove his worth as a strong trainer (Misty and Gary follow) 1st instance of the Rocket Squad being Acro and Astra (WAYYYY stronger than expected) they have gotten what they come for, Aegis and Amity are followed by the supposed leader of Team Rocket being Athena (Lance is oddly late to show up with Loralai and Will having been held up in Lavender Town just missing Rocket Squad)
Flash ahead again to Cinnabar Blaine sends Ash on a funky scavenger hunt into the old mansion to find his lucky lighter (it completely slipped Blaine's mind about what else was happening ghere today and decides to stall Misty and Gary, Brock had left again after getting checked into the Inn the day before) Ash finds Brock but also Athena and Giovanni at the basement having freshly caught something (Mewtwo) Ash is devestated that Brock would side with the enemy so easily (Brock holds Ash back while Giovanni and Athena escape, Brock leaves mid battle with the help of his Kadabra) Blaine battle goes fine albeit Ash is completely deflated
Viridian gym Giovanni decides to make it known that he is the Gym Leader to try to taunt Ash into charging head first (its all a distraction) battle is cut short by Acro informing they have to leave immediately and that preperations are complete (a couple hours later an emergency announcement on the news is made that Indigo Plateu is being invaded by Team Rocket and that Kanto is under emergency lockdown until further notice)
(Fully into B-Plot) Athena has bonded with Articuno and Mewtwo is willing to assist albeit temporarally before it leaves again, Giovanni is one of the best public speakers in the entire region and will hijack said emergency announcement to completely blow the lid on everything (however this hinges on Athena and Aegis being able to take down Lance, if not then it will all be for nothing since Team Rocket is branded as terrorists at this point)
Astra vs Will | Amity and Acro vs Loralai and Karen | Aegis vs Bruno (later turned into Athena and Aegis vs Lance)
Lance for context is using not only his HGSS champion team but also his rematch team at full strength (basically 11 v 12, 11 because Aegis doesnt have a full team)
Lance goes down (Athena and Aegis only had Articuno and Charizard left, Mewtwo had tapped out early due to the mental strain) Athena reveals their identity and it just completely shatters Lance realizing what exactly he had done and tried to do
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Jessie and James did have to explain everything to Ash Gary and Misty while everything went down, Team Rocket were the good guys all along, Brock disnt betray anyone and Lance is the one everyone should be scared of
In the event that Team Rocket's final assault failed Lance would have took that oppritunity to evicerate what good will Kanto and Johto had with eachother to respark the Kanto-Johto War that ended 150 years ago so that Johto could reclaim its right over control of the landmass (at least thats what the Blackthorn Clan Elders had drilled into Lance throughout his life)
Rocket Squad identities, Amity-Erika | Astra-Sabrina | Acro-Janine | Aegis-Brock | Athena-Leaf (btw Leaf uses she/they)
Koga was an undercover squad member having tried getting a position as an Elite 4 years ago but was beat out by Karen after Agatha retired
Surge even though he has a Zapdos really doesnt do much, however he was supposed to be an absolute worst case scenario use (Rocket failed and he was supposed to either hold off the Elite 4 and Lance while everyone who is able to escapes or was supposed to go completely all in if Lance's team was damaged enough to be the final nail in the coffin)
Leaf and Brock dont make it out unscathed both suffering from psychic feedback damage from Mewtwo but also sustaining damage from the final fight (draconic damage has serious side effects later explored in Johto arc) Brock did get hit by a couple stray blows from Bruno's team (Leaf and Brock decide to recover in Pallet since Delia already sees the two as her kids along with Misty and Gary, Leaf used to live in Pallet until her parents moved recently back to Sevii)
Ash and Gary take their Orange Islands trip to reflect on everything while Misty takes it upon herself to help Leaf however she can (Misty is eventually asked to be Loralai's apprentice)
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Ash- Pikachu, Charmeleon, Pidgeot, Kingler, Bulbasaur, Tauros
Gary- Wartortle, Umbreon, Arcanine, Scyther, Nidoking, Magneton
Misty- Starmie, Psyduck, Togetic, Squirtle, Seadra, Seaking
Brock- Charizard, Sandslash, Golem, Sylveon, Kadabra, Onix (also Vulpix but she baby)
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Gary's Scyther is a direct refrence to the Adventures Manga and Magneton is his Yellow champion team
Celadon refrencing Steven's disappearance via international news (timeline following his failed solo Aqua-Magma raid around that time, Kanto takes 1 year Orange isles almost year Johto bit over a year)
Brock's Sylveon is refrencing the gift Eevee in Celadon in every gen 1 game