:3

Your Pokemon and your Partner's Pokemon are paired up together. Each Pokemon is counted as a half. For example, if you get a Blastoise, thats one half. And your partner gets a Charizard, That's the second half, which makes up a whole Pokemon.

What does 'pairing up' the Pokemon, do you ask? Well it makes it so that you can't deposit or withdraw a Pokemon from the PC unless your partner does the same, since they're meant to be one Pokemon. Once pokemon are paired up, they're paired up for life. This also makes it so if your Pokemon faint, your partner's Pokemon will faint too. If your Partner's Pokemon faints while you're in the middle of a battle, you must get rid of the Pokemon as soon as possible.

You're also not able to use a Pokemon unless it's in a pair. So if I catch a Pokemon on route 1, and my partner fails to, I can't use the caught pokemon untill he gets something to pair it up with to make it a whole pokemon.