First you have to beat the game, this means beating dialga at temporal tower.
You have to pass the graduation test, that is in Mystifying Forest. It has 14 floors, and at the end, you need to beat the guild. Wigglytuff is at level 50. Chatot is at level 45. The rest is at level 35. Beware, the pokemon in the dungeons from now on use the items they pick up.
After that step, take a job on the board, and then wait two more days(you can either take jobs or do sentry duty, it doesn't matter). Talk to Mr. Mime to learn about Scizor. Your job is to find him, he was last seen at Blizzard Island. This dungeon has 20 floors. This opens an other dungeon, Crevice Cave. This is where Scizor is found, on the 15th floor. You have to fight Froslass at level 41.
After that, complete an other job, go to bed, then talk to Sunflora to learn about Surrounded sea. This dungeon has 20 floors, and at the end, you find the wonder egg.
The egg will hatch into Manaphy, who will be hungry. You need to feed it a blue gummi. Chatot will mention where to get them, get two. The first time you feed it, Manaphy will be happy, and you take it to sharpedo bluff, where you need to feed it an other gummi. It will then fall asleep. The next day, you take it to the beach. Later, it falls sick, and you need to go get it medicine. This is found in Miracle Sea. It has 23 floors, and at the end, you need to battle a level 46 gyarados. The phione give you the phione dew. Manaphy gets better, and you have to let it go, so it can grow up in the sea, a sad good bye is seen.
Anyway, the next steps are kinda tricky. After that, do one job, and let 3 days pass. On the second floor of the guild, team charm shows up, and you ask to join them on a mission that they are about to do in Aegis cave. This involves many unown. After beating them, there is a 50% chance that they'll drop a stone with their letter on it. There are three stones that have a single word on it. You need to collect those letters and press A next to the stone. If all letters are present, a stair way will open up and you will have to fight a boss. The first one is ICE, and you have to fight Regice(level 46.) There are three floors, and if you don't get all three letters, you can go through those floors again. The second one is ROCK, and at the end you fight regirock(level 46.) There are three floors here as well. The third one is STEEL, and you fight registeel(level 46.) There's four floors here. Once that's completed, you have 5 more floors to travel. At the end of the dungeon, you are joined by Team Charm. You have to battle Regigas(level 49), 4 hitmonlee(level 35), and 4 bronzong(level 35). This opens the concealed ruins.
After beating Regigigas and examining the red stone monument, do one job, and let one day pass, and Cresselia appers in a dream and says that your existence will lead the world to ruin. Do an other job and go to bed, Cresselia appears in your dream again and says that you are someone who must not exist in this world. When you leave your room, you find out that azurill will not wake up. At the guild, in your old room, you discuss ways to wake azurill up. You have to go to Mt. Travail and find drowzee on the 19th floor.
When you find drowzee, you go back to the guild with him. There drowzee will put you in azurills nightmare. This is a dungeon. There are no Kecleon shops, apples, or reviver seeds, so make sure to bring what you need. This dungeon has complex floors and pokemon over level 50. There are 17 floors of the nightmare. Cresselia appears, and it looks like a fight is about to begin, when drowzee shows up, and Cresselia leaves. You leave the nightmare.
Talk to Lapras to find out about Palkia and that lapras can't take you to where it lives. Make sure you have items to go to a hard dungeon before you talk to Lapras. You go to bed, and out of no where, Palkai shows up and takes you to Sky Rift. You run from Palkai. Now you are in the Sky Rift dungeon. There are 25 floors to reach Deep Sky Rift, which has 9 floors. Look out for monster houses, which stats at the 11th floor. Palkia is at level 48. When you defeat Palkia, it enters a nightmare. You can enter its nightmare, where Palkia is going to finish you off. Cresselia appears to finish you off. When a twist happens. Cresselia shows up and reveals that it was really darkrai that you were seeing before. Darkrai challenges you to go to the dark crater. You then go to the guild, and tell everyone about darkrai. Cresselia says that she will go with you, since it's a trap.
Talk to Cresselia near the cliff, when you are ready to leave. There are 15 floors in Dark crater, then there are Deep dark Crater, which has 14 floors. At the end you battle darkrai(level 53,) arbok(level 36,) rhyperior(level 36,) magmortar(level 36,) aggron(level 36,) and magcargo(level 36,) mismagius(level 35.)
After beating darkrai, do a job, and go to bed three times. Manaphy will show up at the beach, and now you can recruit him. Then do an other job, and go to bed three times again, and Manaphy will tell you about Marine Resort.
After all of that, go back to where Palkia is, and recruit it. Then you should be able to evolve the hero and partner pokemon. I think I got this all down correctly, hope it helps.
You have to pass the graduation test, that is in Mystifying Forest. It has 14 floors, and at the end, you need to beat the guild. Wigglytuff is at level 50. Chatot is at level 45. The rest is at level 35. Beware, the pokemon in the dungeons from now on use the items they pick up.
After that step, take a job on the board, and then wait two more days(you can either take jobs or do sentry duty, it doesn't matter). Talk to Mr. Mime to learn about Scizor. Your job is to find him, he was last seen at Blizzard Island. This dungeon has 20 floors. This opens an other dungeon, Crevice Cave. This is where Scizor is found, on the 15th floor. You have to fight Froslass at level 41.
After that, complete an other job, go to bed, then talk to Sunflora to learn about Surrounded sea. This dungeon has 20 floors, and at the end, you find the wonder egg.
The egg will hatch into Manaphy, who will be hungry. You need to feed it a blue gummi. Chatot will mention where to get them, get two. The first time you feed it, Manaphy will be happy, and you take it to sharpedo bluff, where you need to feed it an other gummi. It will then fall asleep. The next day, you take it to the beach. Later, it falls sick, and you need to go get it medicine. This is found in Miracle Sea. It has 23 floors, and at the end, you need to battle a level 46 gyarados. The phione give you the phione dew. Manaphy gets better, and you have to let it go, so it can grow up in the sea, a sad good bye is seen.
Anyway, the next steps are kinda tricky. After that, do one job, and let 3 days pass. On the second floor of the guild, team charm shows up, and you ask to join them on a mission that they are about to do in Aegis cave. This involves many unown. After beating them, there is a 50% chance that they'll drop a stone with their letter on it. There are three stones that have a single word on it. You need to collect those letters and press A next to the stone. If all letters are present, a stair way will open up and you will have to fight a boss. The first one is ICE, and you have to fight Regice(level 46.) There are three floors, and if you don't get all three letters, you can go through those floors again. The second one is ROCK, and at the end you fight regirock(level 46.) There are three floors here as well. The third one is STEEL, and you fight registeel(level 46.) There's four floors here. Once that's completed, you have 5 more floors to travel. At the end of the dungeon, you are joined by Team Charm. You have to battle Regigas(level 49), 4 hitmonlee(level 35), and 4 bronzong(level 35). This opens the concealed ruins.
After beating Regigigas and examining the red stone monument, do one job, and let one day pass, and Cresselia appers in a dream and says that your existence will lead the world to ruin. Do an other job and go to bed, Cresselia appears in your dream again and says that you are someone who must not exist in this world. When you leave your room, you find out that azurill will not wake up. At the guild, in your old room, you discuss ways to wake azurill up. You have to go to Mt. Travail and find drowzee on the 19th floor.
When you find drowzee, you go back to the guild with him. There drowzee will put you in azurills nightmare. This is a dungeon. There are no Kecleon shops, apples, or reviver seeds, so make sure to bring what you need. This dungeon has complex floors and pokemon over level 50. There are 17 floors of the nightmare. Cresselia appears, and it looks like a fight is about to begin, when drowzee shows up, and Cresselia leaves. You leave the nightmare.
Talk to Lapras to find out about Palkia and that lapras can't take you to where it lives. Make sure you have items to go to a hard dungeon before you talk to Lapras. You go to bed, and out of no where, Palkai shows up and takes you to Sky Rift. You run from Palkai. Now you are in the Sky Rift dungeon. There are 25 floors to reach Deep Sky Rift, which has 9 floors. Look out for monster houses, which stats at the 11th floor. Palkia is at level 48. When you defeat Palkia, it enters a nightmare. You can enter its nightmare, where Palkia is going to finish you off. Cresselia appears to finish you off. When a twist happens. Cresselia shows up and reveals that it was really darkrai that you were seeing before. Darkrai challenges you to go to the dark crater. You then go to the guild, and tell everyone about darkrai. Cresselia says that she will go with you, since it's a trap.
Talk to Cresselia near the cliff, when you are ready to leave. There are 15 floors in Dark crater, then there are Deep dark Crater, which has 14 floors. At the end you battle darkrai(level 53,) arbok(level 36,) rhyperior(level 36,) magmortar(level 36,) aggron(level 36,) and magcargo(level 36,) mismagius(level 35.)
After beating darkrai, do a job, and go to bed three times. Manaphy will show up at the beach, and now you can recruit him. Then do an other job, and go to bed three times again, and Manaphy will tell you about Marine Resort.
After all of that, go back to where Palkia is, and recruit it. Then you should be able to evolve the hero and partner pokemon. I think I got this all down correctly, hope it helps.
