Currently how my Pokemon game is set up, I have a command named Set. Set changes the game pov so the player turns into a Pokemon. I'm not sure how Pokemon does it exactly. I don't like it, but it's better than the player wielding Chikorita like a pistol like my I'd code...
Set command:

msg ("You are now " + object.alias + "!")
game.pov = object
MoveObject (player, Game Over1)

Do you have an example of what you're trying to achieve?

This is a Let's Play of Pokemon, to those unfamiliar with it. https://www.youtube.com/watch?v=9mVTjGfyEnw&list=PLE3C86AE5AD25B11E

I did find the entirety of a Pokemon game in complete JavaScript. https://github.com/loic-sharma/Pokemon
Edit reason: Posted the wrong game earlier.

Alright, so far I might just have to bring in the teleport to a different room functions from my Dante's Inferno game and then I can make the player invisible instead of just moving him to a different room. I've gotten that far at least.

I made a thread on 4chan's /wsr/ board about it and all I got back was about memory.

There are tons of examples of Pokémon DIY setups online, mostly because all of the code for the battle system, etc is well documented by sites like Bulbapedia. I'd try googling stuff along the lines of 'make your own pokémon game' and start from there.

Making an imitation of the Ruby/Sapphire battle system was one of the first battle systems I made myself, come to think of it. That was years ago though, and horribly inefficient.

Where is the battle system on Bulbapedia? I can't find anything besides glitch descriptions...

Okay, I got something. What about a Pokemon object list, and you can just turn into any Pokemon in that list.
How the player interacts with that list, however, I don't know...