Charizard was in the Old Amber. Abby has returned. (at Level 5, but whatever)
The true identity of the Dome was Ariados.
Shellock Holmes is a Blastoise.
The too-weak Swablu is now a majestic Altaria.
Firered is being played on a ROM hack that randomizes everything from Pokemon to even their movesets. All the starters and wild Pokemon are completely random with randomized abilities and moves, the latter of which are usually adhering to that Pokemon's type (e.g. Psychic Pokemon suffer in this RNG because they have too many non-damaging moves in gen 3). Also, all the gym leaders and trainers have randomized Pokemon teams.
To summarize some notable events:
Their starter was a "Bulbasaur" that turned out to be a lazy Machop with the ability Truant (it attacks every other turn).
Route 1 was filled with armless Pokemon (re: Slugma, Taillow, etc.) that all had punch movesets.
More hilarious shenanigans I'm too lazy to type out.
For their legendary encounters:
They traded a Nidoran Male for a Mew. Totally a fair trade.
"Moltres" turned out to be a Latios, which they defeated.
"Zapdos" turned out to be a Mewtwo, which they ran away from.
"Articuno" turned out to be a Mew, which selfdestructed.
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