PokéBase - Pokémon Q&A
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I was just watching a video of someone starting a new game on Emerald, and when the professor was being attacked by the Zigzagoon, and you look in his bag, the Pokemon were Lanturn, Blastoise, and another water Pokemon. Why weren't they the starters? When I played it, I remember them being torchic, mudkip and treeko.

The person making the video then went into some tall grass and encountered a meganium and a groovile. Was he using an action replay or something? I couldn't tell, because the microphone on my computer isn't working.

Or am I just missing something massive here?

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Maybe it was something else like randomizer he was playing. Otherwise his game's glitched up.
What's randomizer?

Actually, he did have randomizer in the title...

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If he was playing online, randomizer is a version of the game on an emulator (so automatically a ROM file) that completely randomizes:

   - Starter Pokemon & their items
   - Wild Pokemon, including event Pokemon
   - All other in-game Pokemon, including trades and prizes
   - Trainer Pokemon
   - Trainer titles (like 'Lass' or 'Pokemaniac')
   - Items found on the map, including hidden items
   - TM attacks
   - Pokemon-TM compatability
   - Pokemon themselves, including types, stats, palettes, abilities,
       wild hold items, and movesets
   - Redefining certain evolutions so trading is not required
   - Changing some core game things, like stacking TMs in groups of 90,
       starting with the National Pokedex, or modifying store stocks.

Source
Hope I helped!

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it's kinda fun sometimes to take such challenges, it feels like taking a vacation from pokemon logic
That sounds so fun! Too bad emulators are illegal though. :P
I never knew they were illegal. Thankfully I haven't downloaded any then
Emulators aren't illegal as far as I know. It's if you play a game on one that you don't legally own a physical copy of on an emulator that makes it illegal.
So if you played FireRed on an emulator and you never owned a legit copy of the game, then yeah, it's illegal. But I don't know of anyone who got caught.