The Pokémon Center Secret

I've always assumed it works the same as the anime, where Nurse Joy takes your Pokémon, treats them, and returns them to you later. Except the animation is a lot faster in the games so it's not super annoying or inconvenient, heheh. But that's just me and my thought process o:

 

Since Ash isn't actually part of the games, they are different protagonist and rival, maybe they have created a machine between the time of the anime and the time of the video games. Or they exist is two different Pokémon universes, since there are some very noticeable differences between the anime world and the Video Game world.

 

I always figured it was tired to the Pokéball technology, since the Pokémon had to be in their balls, as shown in HGSS where if they were following you they'd have to go into their Pokéball.

 

Since we don't know much about PokéBalls we really can't say since there is already the question of how the hell do PokéBalls work? They defy physics as is so yeah. Really I can't say.

 

K' the Pokémon are taken to a realm of infinite happiness, ergo the PC, where they take a new physical form and become digimon. The digimon are now dumped in the garbage and you receive a PokeClone. Nurse Joy is the most evil person in the game. Mewtwo should have stopped this and fainted digimon become (t)rubbish. The end yeeeeeeee

 

Your Pokeballs are taken and they, along with your Pokémon, are destroyed.

Then Nurse Joy gives you some new Pokémon.

 

This.
This theory wins.

 

Nurse Joy is evil, and she wants your Pokémon to be hurt over and over!!!

 

Nurse Joy takes your balls, brings them back to "health" and you leave with a smile on your face.
What? You thought I was suggesting something perverted, I am ashamed of you! Get your mind out of the gutter man.
Yes, that sentence was an innuendo Tehe

 

As far as I can tell, it's been hinted at that Pokémon become digital energy etc. inside Pokeballs. So maybe, the machine sort of "jacks" in to the Pokéball, reads the data, checks for low health, if it's there then the machine restores it! That's my theory.

 

I bet that Nurse Joy had a fallout with a trainer once, so now she wants all trainers and their Pokémon to suffer!

 

Hey, at least you don't have to go to med school. Poor Joy... she probably went for her PHD, then the healing machine got invented. Now she gets paid minimum wage.

Anyways, they probably jack the machine up with Potions and other PokeMedicine that then transmits through electrical wires in the machine. Wonder what it would feel like to stick your hand in there. Hmm...