So, assuming you've beaten Beta 2, picking up right where it left off, we last found out that apparently, the purple rock at the Pewter Museum has been stolen (if you actually go to the Pewter Museum in-game, you'll notice that I accounted for that, and it is indeed missing) and that Daisy wants to meet at Cinnabar Island (and yes, I accounted for that too, she won't be in her gym). Green (or Red if you played as a girl) said that it was probably Kamon.
As soon as you reach Cinnabar Island, you would have encountered Daisy once more, and she agrees that it was most likely Kamon who stole the purple rock from the museum. Daisy suspects that Kamon would have taken it to Birth Island (how he got there, he probably used some Team Rocket transportation), so then Red, Blue, Green, and Daisy all go to Birth Island (Daisy will have a boat parked at Cinnabar similar to how Bill had one in FR/LG for the Sevii Islands).
Upon entering Birth Island (it would have looked exactly the same as in Emerald), as predicted, Kamon would be there, make a small speech about his motivations and how what he's doing is for the greater good, saying that it's better in his hands than Giovanni's. So then you literally watch Kamon complete the Birth Island puzzle, and purple rock would appear and form into Deoxys, and Kamon would immediately capture Deoxys with a Master Ball that he stole from Silph Co., while Red, Green, Blue, and Daisy can't do anything about it. Kamon will then triumphantly claim that he has saved Kanto and that the Devil's Prism is now useless. (He will also mention that he stole a 2nd Master Ball and that he no longer has any use for it, and upon leaving a Master Ball will be left behind, in which you are free to claim). So now that Kamon has captured Deoxys, it seems all is lost.
Then you head back to Cinnabar and as usual, you need the Secret Key to enter Blaine's Gym, so you head into the Pokémon Mansion. However, unlike usual, there is only one diary this time (the diary entries would have been exactly the same but with translation fixes thanks to Bulbapedia, just compiled together as one diary rather than spread out across several). Upon reaching the diary, Ariana and Archer would be there, and Archer will mention that Giovanni has finally located the legendary Pokémon (but didn't Kamon capture Deoxys already?) Then you find out from Archer that the legendary Pokémon that Giovanni is searching for is the one that burned down the Pokémon Mansion thirteen years ago, and killed Giovanni's wife, leaving Kamon a motherless child. And apparently, this legendary Pokémon completely obliterated another Pokémon of similar power. Archer then says his last words in the game, and bids farewell, saying that Team Rocket will win.
After getting the key, you go into the Cinnabar Gym and battle Blaine to get your final Badge. His team was intended to be Arcanine, Ninetales, Rapidash, and Magmortar.
After getting the Volcano Badge, Green would inform you that Mr. Fuji has arrived at Cinnabar Island and has an important message to pass on to Red, Green, and Blue.
Upon going into the Cinnabar Lab in one of the rooms, you'll see Fuji, who will then tell you the story about a scientist who discovered and cloned Mew (he'll subtly imply that he was the scientist, because he actually was). In my canon, Mew was impregnated and gave birth to Mewtwo, as the diary entries in the original games imply, and was cloned by somatic cell nuclear transfer.
After Mewtwo was born in February, it had grown far too powerful for Fuji and helpers to contain by September, and thus Mewtwo escaped, burned down the mansion, and then went on to cause the Great Tohjo Purge that was mentioned occasionally in the game (Giovanni's wife died during this time).
We learn that around this time, somebody discovered the existence of a Pokémon called Deoxys, and unleashed it at Birth Island to put an end to Mewtwo. Eventually, Mewtwo and Deoxys crossed paths, but Mewtwo was more powerful and completely destroyed Deoxys's body, leaving only the crystalline organ that was in its chest (aka "the purple rock"). Mewtwo was weakened from its fight with Deoxys, so it retreated in a nearby cave (Cerulean Cave), while the remains of Deoxys was eventually found and put on for display in Pewter Museum.
Back in present time, Mr. Fuji tells Red/Green/Blue that he thinks Mewtwo is the legendary Pokémon that Giovanni was looking for this whole time, NOT Deoxys (Hint: notice how in-game, Giovanni never actually says 'Deoxys').
After Fuji is done telling his story, a Team Rocket Grunt would have burst in (and he would be scared as well for obvious reasons) saying that he has a note from Giovanni to Red (the player). The note would basically say the Devil's Prism is complete but he needs the Legendary Pokémon in order to activate it. He claims that Kamon told him that Red stole the Master Balls from him, and orders Red to immediately head to Cerulean Cave to give him a Master Ball. Even if Red doesn't, Giovanni has already ordered his scientists to develop their own Master Ball using info stolen during the Silph invasion, and that either way he'll capture the legendary Pokémon (Mewtwo) eventually, but if Red hands him one now, then he won't be "punished".
Red, Green, and Blue all agree that they don't have any choice but to head to Cerulean Cave. Mr. Fuji suggests that maybe, just maybe, Red could capture Mewtwo using the Master Ball, and prevent Giovanni from using it for his evil purposes.
Red, Green, and Blue enter Cerulean Cave (well gameplay wise, they'll enter first and you'll meet up with them time to time and they'll heal your Pokémon when you need them to). At some point Red (the player) is stopped by Kamon, who claims that he already captured the legendary Pokémon, and that he's the only one that can stop Giovanni.
Eventually you'll make your way to a small chamber where you'll see Mewtwo, but with the Devil's Prism behind it (Giovanni had the Devil's Prism transported there), although the Devil's Prism would look a lot different from the glimpse at the Rocket Hideout, since it is now complete. Giovanni would arrive and express his gratitude that you are there, saying he needs this Pokémon (Mewtwo) so he can use its power through the Prism so that he can rule over Kanto without opposition (basically the Devil's Prism combined with Mewtwo's psychic abilities would enable Giovanni to have superhuman abilities).
Then Mewtwo will suddenly walk up you and you'll suddenly be in a battle with it. It would have its own theme composed by me, though I wanted to include parts of the Mega Charizard X theme from Pokémon Origins, since Mewtwo was a big part of that scene. This is a mandatory capture, it will simply respawn if you defeat/run from it. Then you are given the option of opening your PC to place Mewtwo into your party, with the suggestion of having it at the front.
So Red just captured Mewtwo and now Giovanni's all pissed off, and then Kamon appears and expressed his opinion to his father that his father's methods of revenge are wrong, and that he tried capturing the legendary himself, except that he thought Giovanni was looking for Deoxys, not Mewtwo. But Kamon captured Deoxys already lol. Giovanni is shocked, saying that Mewtwo killed Deoxys thirteen years ago, and that Kamon must be lying. But Kamon says he'll prove it.
Then Kamon will basically say he doesn't like you (lol) and then challenge you one final time (his battle theme will be more intense than before). He'll send out Deoxys first. And then it's intended that you placed Mewtwo at the front of your party, so you'll send out Mewtwo first. It's literally Mewtwo vs. Deoxys.
Red beats Kamon, then Giovanni gets more pissed and battles you one final time, but his battle music will also be more intense and final-battle-like. Giovanni will reveal that it was he who unleashed Deoxys thirteen years ago, and that he intended for Deoxys to kill/badly hurt Mewtwo, but Mewtwo ended up destroying Deoxys's body instead.
After Red beats Giovanni, Giovanni then realizes that Red's bond with his Pokémon is what gave him this victory, and that Giovanni failed to capture Mewtwo as he could never love Mewtwo as a Pokémon, because Mewtwo was responsible for the death of his wife. Giovanni then disbands Team Rocket and leaves.
Kamon, being three years younger than Red and more immature, then thinks his Pokémon are weak because he's lost to Red so many times and how he hates the weak, so he says he has no use for his Pokémon (thus hinting that he will release them all, giving him a fresh start in the planned DarkCrystal Johto remake). Then Kamon leaves and Blue and Green are all "yay you did it you're awesome" and stuff and they all live happily ever after
So you have 8 Badges, you enter Route 22, battle Blue as usual, and then you're about to enter the road to the Pokémon League but then you see Giovanni and Kamon (just like they were in the HG/SS Celebi cutscene). Then the HG/SS Celebi cutscene plays out, word-for-word (but with some minor dialogue adjustments to account for DarkViolet's story). Except Kamon will then speak to you one last time and tell you about his new motivations and reveal that he's released all of his current Pokémon (including Deoxys, so you're free to capture it postgame).
The rest is same old, same old. Except, right before you enter Victory Road, Green (or Red if you're playing as a girl) appears and challenges you. Her team is:
Nidoqueen (Nidoking if battling Red)
Clefable
Dragonair
Scizor
Vaporeon / Leafeon / Flareon
Venusaur / Charizard / Blastoise
Then you go through Victory Road (Moltres is back here, at Lv57 like with Zapdos and Articuno).
The Elite Four will be like in the newer official games, in which you can challenge them in any order you want. The teams would have been:
LORELEI:
- Dewgong
- Cloyster
- Glaceon
- Jynx
- Lapras
BRUNO:
- Primeape
- Hitmontop
- Hitmonchan
- Hitmonlee
- Machamp
AGATHA: (officially rebranded as a Poison-type trainer)
- Crobat
- Arbok
- Tentacruel
- Muk
- Gengar
LANCE:
- Gyarados
- Kingdra
- Aerodactyl
- Altaria
- Dragonite
BLUE:
- Pidgeot
- Machamp
- Rhyperior
- Exeggutor / Arcanine / Gyarados
- Arcanine / Gyarados / Exeggutor
- Blastoise / Venusaur / Charizard
In the original Pokémon games, Blue gained a jacket in his sprite for the Champion battle. As a nod to this, my plan was for him to have his HG/SS design for the Champion battle (he has the FR/LG design for most of the game).
And then there would have been a postgame area designed by me as well as a custom battle facility similar to Black Tower/White Tree Hollow.
Heatran, Deoxys, and Mew are the postgame legendaries. Heatran would have been caught at a new postgame mountain area, Deoxys at Birth Island, and Mew at Faraway Island. Heatran would have actually used the vanilla FR/LG legendary theme, NOT the theme I made for the birds alone. Deoxys would have had the same theme as he does in FR/LG/Em. Mew would have had Mewtwo's battle theme.
