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In the game, PC boxes are 6x5, and therefore can hold 30 Pokémon each. Since there are 18 of them, you are able to hold a total of 540 Pokémon in your boxes.
It was around the time Gold and Silver were out that I started having thoughts about having a copy of every Pokémon in the PC. Of course, I never actually did do it, moreso due to laziness than a lack of obsessiveness. The thought periodically cropped up as I continued to play through the games over and over, and Diamond and Pearl was no exception.
So as I stated, you can hold 540 Pokémon in the boxes. There are 493 Pokémon, so if you want to get a copy of every one of them, you can comfortably fit them all within the boxes. You'll end up with 47 spaces to spare.
But wait! There are certain Pokémon that have alternate forms to them. shinies, gender differences, the ridiculous amount of Spinda variations...I excluded those from the count. But there are still others out there, that aren't any of these, that one might want to collect.
Unown is one that immediately comes to mind - it has 28 forms. Since one of them is already accounted for in the initial Pokémon count, we subtract 27 from 47 to get the amount of space remaining. 20 slots.
But then there's Burmy and Wormadam to consider. They have three forms each. Again, since two of these are accounted for in the initial count, we subtract four from 20, and end up with 16.
Then there's Shellos and Gastrodon. That's another two. We're at 14 now. Deoxys is also included as having multiple forms. Getting by the difficulty of obtaining four of them, we'd end up with 11 slots. So what else is there?
Arceus.
It has 17 forms in total. Again, getting by the difficulty of obtaining 17 of them, one is accounted for, so we subtract 16 from 11 and end up with -5.
Remember, you have room for up to six Pokémon in your party. So really, you can hold up to 546 at a time. Add six to -5 and you have one. One empty slot, and a whole variety of explanations.
One that I found interesting was Arceus' unused ??? type form. If it were obtainable, all the slots would be able to be filled up. It's not though, so you have a spare slot to do whatever you want with. Another possible explanation is that this extra slot is so that you can get eggs from the daycare. Without that slot, you'd have no room. Or, maybe it was for that, and for the general catching of anything you desire.
It can also be noted that if you really want to look at the big picture, you have another three slots - two in the daycare, and one in the GTS. Although they're hardly stable; daycare Pokémon level up in there and may have their movesets ruined (although this can be circumvented with Level 100s or ones that don't matter if they level, such as Ditto), and the GTS Pokémon may be traded or purged after not being traded for so long.
What is that empty slot really for? I don't know. Am I the first to notice this? I don't know. Was this intentional, or just a really big coincidence? I don't know. All I know is that it works, and that looking deep into things may reveal information that you might not want to know.
It was around the time Gold and Silver were out that I started having thoughts about having a copy of every Pokémon in the PC. Of course, I never actually did do it, moreso due to laziness than a lack of obsessiveness. The thought periodically cropped up as I continued to play through the games over and over, and Diamond and Pearl was no exception.
So as I stated, you can hold 540 Pokémon in the boxes. There are 493 Pokémon, so if you want to get a copy of every one of them, you can comfortably fit them all within the boxes. You'll end up with 47 spaces to spare.
But wait! There are certain Pokémon that have alternate forms to them. shinies, gender differences, the ridiculous amount of Spinda variations...I excluded those from the count. But there are still others out there, that aren't any of these, that one might want to collect.
Unown is one that immediately comes to mind - it has 28 forms. Since one of them is already accounted for in the initial Pokémon count, we subtract 27 from 47 to get the amount of space remaining. 20 slots.
But then there's Burmy and Wormadam to consider. They have three forms each. Again, since two of these are accounted for in the initial count, we subtract four from 20, and end up with 16.
Then there's Shellos and Gastrodon. That's another two. We're at 14 now. Deoxys is also included as having multiple forms. Getting by the difficulty of obtaining four of them, we'd end up with 11 slots. So what else is there?
Arceus.
It has 17 forms in total. Again, getting by the difficulty of obtaining 17 of them, one is accounted for, so we subtract 16 from 11 and end up with -5.
Remember, you have room for up to six Pokémon in your party. So really, you can hold up to 546 at a time. Add six to -5 and you have one. One empty slot, and a whole variety of explanations.
One that I found interesting was Arceus' unused ??? type form. If it were obtainable, all the slots would be able to be filled up. It's not though, so you have a spare slot to do whatever you want with. Another possible explanation is that this extra slot is so that you can get eggs from the daycare. Without that slot, you'd have no room. Or, maybe it was for that, and for the general catching of anything you desire.
It can also be noted that if you really want to look at the big picture, you have another three slots - two in the daycare, and one in the GTS. Although they're hardly stable; daycare Pokémon level up in there and may have their movesets ruined (although this can be circumvented with Level 100s or ones that don't matter if they level, such as Ditto), and the GTS Pokémon may be traded or purged after not being traded for so long.
What is that empty slot really for? I don't know. Am I the first to notice this? I don't know. Was this intentional, or just a really big coincidence? I don't know. All I know is that it works, and that looking deep into things may reveal information that you might not want to know.