you have to go to the surrounded sea and when you get to the end you will find 2 deluxe boxes and an egg. take the egg and you will get manaphy! It only eats blue gummis so if you have some - great! If you don't. go back to a sea dungeon and you will find some. Manaphy goes away but will come back later.
you will have to get the wonder egg at the surround sea. it will hatch into manaphy. and you would have to feed it some blue gummis. soon it will get sick and you will have to get the phione dew at the end of miracle sea. then it will have to leave you for a while. after you have beaten darkrai (the true final boss) manaphy will return and ask to join your team.
Keep playing the adventure and eventually after Manaphy leaves with Walrein, it will come back one morning and will ask to join your team.
you need to finish the whole game then do a couple mission and after that manaphy comes and tells you that he wants to be a guild member
just progress through the story mode.
Manaphy returns some time after you defeat Darkrai.
two
a few days after manaphy comes back
you get them in missions. in surrounded sea you get manaphy, although you cant recruit him.
you have to defeat darkrai and have cressilea,manaphy and palkia on your team
you go to surrounded sea and complete the dungeon and find an egg.at home it hatches and becomes manaphy.
Manaphy isn't in this game he's in mystery dungeon explorers of Time & darkness or Sky
after you go on a few missions after manaphy leaves (spoiler alert!:Manaphy comes back but at level 40 after you defeat darkrai and you are able to evolve)
wait a couple of days after manaphy joins ur team and manaphy will tell u about the gummi full marine resort!
Well you have to defeat darkai and you have to raise manaphy :D That's always fun.
after you finish manaphy mission they will be in the guld later on the bottem floor
Just go about your rescue business for a bit. As I recall, after Darkrai, the next major event is Manaphy returning.