go to much dungeons and after some time chatot wil come to sharpedo bluf and tel you that manaphy is on the beach
after setting manaphy free, complete the following events and beating Darkrai, Manaphy will return.
When you PWNED Darkrai, after a few stupid jobs, Manaphy will come back He ain't found in a dungeon. He will join you immediately.
wait three days, do one job, and recruit palkia. manaphy should either come up to you or be on the beach. must be after you beat darkrai.
In the actual story, you have to defeat Darkrai. However after that Manaphy will wan't to join the team, and he will unlock a dungeon called Marine Resort.
evolve,and recycle until you get a new place
Deep Dark Crater B12F which is the level after the Manaphy and Phione Level in the Miracle Sea, after that, when you go into Azurill's nightmare, the level which is after that is the level where you have to find Darkrai
After you beat darkrai, wait a few day's then after you recuite manaphy, wait a few more days and then manaphy tells you about marine resort, then darkrai will appear at mystifying forest 13f,miracle sea b3f, lower crevice cave b2f, mt. travil 17f, special rift b14f.
Just go about your rescue business for a bit. As I recall, after Darkrai, the next major event is Manaphy returning.
Manaphy will have to leave because chatot said so and also because he can not live without being in the ocean but don't worry becuz after you beat darkrai manaphy will come back and join your team in 3 days or so
well you pretty much beat the game. you can also evolve. oh and you get manaphy and cresselia on your team.
when you beat darkrai in Pokemon mystery dungeon 2 do like 10 more missions on the next morning after you wake up chatot will tell you that manaphy came back and she will ask you if she could join your team
After a little while into the post game, Cresselia starts appearing into your dreams or at least Darkrai is. He was pretending to be Cresselia. Cresselia is really good, but the Cresselia in the dreams are Darkrai's doing.