After you beat the game 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. This to be honest is quite a challange and it took me a long time to do this.
After that step, take a job on the board, and then wait two more days, Mr. Mime will appear, speak to him 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, which is also a challange
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 (pain in the butt mission). 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 more difficult. 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. (I recommend not to carry items to this dungeons – maybe lots of apples it will take a while and use the recruitment list to your advantage for letters) The first one is ICE, and you have to fight Regice 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. 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, 4 hitmonlee and 4 bronzong. (very evil) This opens the concealed ruins. (P.S have many reviver seeds in this dungeon the final battle is very evil as I mentioned)
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 starts at the 11th floor. Palkia. 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, arbok, rhyperior, magmortar, aggron and magcargo and mismagius. (this is so hard as darkrai has ominous wind which is super effective on cressila and if cressila faints you have to start again as if it was your partner
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. (you don’t have to go here)
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 will know if you can evolve because your partner will mention it in a conversation)