after you beat dialga you so some things, then you get a manaphy egg. It hatches the next day, then a little while longer it has to go away. Then you start having "creselia" in your dreams, a little later she tells you you need to be destroyed because you are doing something or another to space. You have more dreams and stuff, yada yada rada rada THEN, palkia shows up at your house and takes you to spacial rift. After that you figure out that the "creselia" in your dreams is realy darkrai. And that darkrai was preventing the worlds paralizes. Then you go beat him.
Then comes the legendaries. in dongeons on floors -not the end of the dongeon- but you need a reqruitment item that raises the rate and a secret slab.
Heres a wonder mail code fo the secret slab: &CR6 WRFT @J1T
6-P@ S1W@ %@-#