Manaphy was a rather elusive, and difficult Mythical Pokemon to get back in the day.
The only way to obtain a Manaphy Egg was to have a copy of Pokemon Ranger that hadn't completed the Manaphy Mission on it already. This mission was once per cartridge only. The easiest way to get the mission unlocked was on the original game, as it did not require wi-fi to get it, but a code, and had unlimited availability, unlike the other two games after it in the franchise. Anyway, if you were able to complete this mission, you can send a Manaphy Egg to your games in D/P/PT and HG/SS only. The egg cannot be sent to B/W or B2/W2. This is also the only way to easily get Phione, as well, as breeding Manaphy with a Ditto (or another Manaphy? but idk about that) will give you a Phione.
Did you ever bother trying to get Manaphy in the Fourth Generation games? I did actually bother, once. I just happened to have a used copy of the original Pokemon Ranger that hadn't completed the Manaphy Mission or even had it unlocked. So, I was able to complete it & send Manaphy over with Mystery Gift. Honestly, it was a one time experience I'll never be able to do again, and I'm glad I did it.I hope they don't do something like this ever again, though. Having to buy some spinoff just to get a mythical Pokemon is annoying.
i legit only wanted pokemon ranger for this reason, yet never did it. i hated ranger and got stuck fairly early on so lmfao eff that i guess. i had a hacked manaphy in diamond eventually, if that counts or matters for anything. don't really care for manaphy much and it seems kind of meh to me. phione is cuter, but i can't fully like that one either bc i feel like its only purpose is just so there's a gimmicky legendary that gamefreak can be like 'oh this is the only breedable legendary!!' and it's just. dumb. cute. but dumb.
I technically have a Manaphy. Rather, I have a Pokémon Ranger cartridge from when I was a kid that never had the Manaphy taken out. I would finish the game and move it over, but damn, I can't stand playing Ranger. The circle drawing stuff really kills my wrist, and the save that's on the cartridge at the moment is seemingly in a bad spot. I'm pretty sure it's near the end of the game, but I'm super weak. None of the Pokémon I have in my team are relevant to the area I'm in and I have no idea what I'm supposed to be doing.
That's kinda how I got Manaphy myself. I found an old Ranger cart, used it to send Manaphy to my game and lost the cart. Then sometime between gen 4 and when I really got back into Pokemon in gen 6, the original Manaphy was...no where to be found. I couldn't remember if I had traded it or something for the life of me (I must've, as I would have recieved an event Manaphy by then and probably thought the original was good trade fodder) and it still saddens me to this day due to how rare it is. If I manage to track down a Ranger cart again, I'd have to try RNG abuse to be able to get a shiny one for my collection!