after you complete the darkari mission sleep for a few days and manaphy will come back and join your team
little edit:Manaphy will also tell you a new place to explore marine resort. Good luck!
wait fifteen through twenty days and he will come back
Advance the storyline. They do come back to join you eventually.
I don't Know Because im trying to find out myself
i think you finish the darkrai mission then wait a few days and manaphy should join
a few days after manaphy comes back
Just go about your rescue business for a bit. As I recall, after Darkrai, the next major event is Manaphy returning.
Manaphy returns some time after you defeat Darkrai.
two
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)
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
wait a couple of days after manaphy joins ur team and manaphy will tell u about the gummi full marine resort!
You have to beat the game them defeat dakari amd palkia and reggigas and few others so then you get manaphy and manphy comes back then you could evolve
Just keep on doing jobs, and eventually, cresselia will appear in your dreams, and the story line will move on, getting near the end.