you find a egg in the surronded sea and the next day it hatchs into manaphy
after you find and lose manaphy, help team charm, and do several more missions
after that you gotta find manaphy and it gives you the location of marine resort
Shimmer Desert
you go to surrounded sea and complete the dungeon and find an egg.at home it hatches and becomes manaphy.
You find him in spacial rift.
Mount Avalanch floor 20
dark crater
In Pokemon: Mystery Dungeon Explorers of Time/Darkness, Moon Stones can be found rarely in Kecleon Shops for 2000 Poke.
I am not completely sure if this works on Explorers of Darkness, but here is a way: after beating Primal Dialga, and after some days of random missions, you will find a egg. the egg contains the Pokemon Manaphy. if you choose to take care of him, and contiunue until he leaves, he will later return, and he has grown up. when he does that, he tells you about Marine Resort, and makes you able to go there.
In Pokemon Mystery Dungeon: Explorers of Darkness, the Golden Apple is a rare item you can find in Treasure Hunts. It is also an item you can find in the Golden Chamber which is a rare area to find in dungeons.
after manaphy returnes to the sea azurill starts having nightmares so you need to go find drowzie and he helps you after you find him
U find Darkrai in Dark Crater.