go through the marine resort. once thats good to go, Manaphy returned right? and have you also evolved your starter / partner yet? just continue for a few missions in the game, you'll start to come across Cresselia and Darkrai and such. Palkia also should show up, so you'll get to finish the last half of the game. Just keep doing missions until the event pops up. its always going to be do missions for the next segment of the game. :P
Yo.