Ok, I have been having trouble after I defeated Misty. After I save, I save quite a lot every now and then, I got off the game for the day. The next day, I had only 1 badge still, My two Pokémon, Bubasaur and Charmander were gone, and I didn't even beat my rival yet! Does anyone know the problem of this?

I'm very certain that Pokemon does not auto-save, like most adventure games. Have you saved before turning off? I've done it a few times, where I do so much in a session of game play, then turn off the power before realizing I forgot to save all that hard work and progress! Yes, it's a pain, but it's also good for undoing heavy mistakes you make in the game. And I'm very certain some people have done that in a game like Pokemon (I once used all my Pokedollars to buy loads of Lemonade for the fun of it, then realized I needed that money for a bicycle.)

None of the Pokemon games auto-saved.  I do wish it did on key events, like after defeating a gym leader, like you did, or even after exiting Palette town. The first time I played, I had to go through all that dialogue all over again because I turned off power and didn't know there was a save feature included, since it doesn't auto-save! Silly me..

I wish I could help you get back the game progress you lost, but I can't do much about it; I'm far away from you because of the internet and the game is already turned off anyway.

Yes, I have been saving before turning off the game though the three times I've went to the same save station before defeating Misty. I've always been doing that in my Pokémon games. Unless, I have to buy the bike before I go any further. Anyways, thanks for the help.

You don't buy the bike.  You get a bike voucher from the Pokémon fan club man and you get a bike for free. 

PikaPokeFan123 : you need to get either electric or grass type pokemon to beat misty. Shes the easiest to beat when you first start out.

PikaPokeFan123 : Are you using the RGR plugin with save states? Or are you just saving IN-game?

There is no way for me to get back your data if it is lost, but I will say that you should always use F2 to save as a backup even if you only want to save in-game as the game was originally programmed. To load hit F4. Save states let you save at any point of the game so it is nice to use this feature. That way you almost are always assured to have your data.

Also were the initial saves made before the RGR plugin update was installed and the load after you installed it? Just wondering