RayquazaSpawn

It's a long explanation, so brace yourself!
You must do a few optional missions (or roam in dungeons), then eventually when you stop by the guild, Team Charm will be there, talk to them, they tell you about Aegis Cave. After that go there, the first cave you must find the I, C, and E unown stones and fight Regice, then the R, O, C, K stones and fight Regirock, then deal with the S, T, E, E, L stones and fight Registeel. After that you must go through the Aegis Pit. In Regigigas' Chamber, you'll team up with Team Charm. Be careful! There'll also be four Bronzongs and four Hitmonlees (your best bet is to bring your Dialga with you, It's roar of Time will do the trick!) After taking care of every one of them, that objective will be complete. (don't worry about the newly unlocked dungeon.)
Next, after a few optional missions, Azurill will be envleloped in a deep nightmare. You must head to Mt. Travail (Careful, you can only bring You and your partner). After speaking to Drowzee, You will be asked to go into Azurill's Nightmare, after you do so and speak to Lapras after a few cut scenes, Palkia will warp you to the Spacial Rift. You must Defeat Palkia at the end of the dungeon. After meeting the real Cresselia, You will finally go to the Dark Crater, at the pit you will face Darkrai, along with him is Rhyperior, Arbok, Magcargo, Magmortar, Aggron, and Mismagius (don't worry, Cresselia will be with you). You MUST defeat all of them and Darkrai to win. The difficulty is based on how your team's built.