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After the credits you end up back at the guild, only that today is your graduation exam. Wigglytuff tells you that you will have to fight Grand Master of All Things Bad and put the Treasure of the dungeon in a place called Luminous Springs. As you get ready in treasure town you meet tediusa and Ursaring who tell you they play there all the time. When you get at the end of the dungeon, you fall in a pitfall trap, into a dark cavern. Where you fight the Grand Master of all Things Bad and his minions, who turn out to be Wigglytuff and the guild members but they act like if they arent. After you beat them you see the spring in which Teddiursa steps into and Evolves into Ursaring but when your partner steps into it it says you and your partner cant evolve yet. You need to at least Recruit Palkia, the ruler of space. For now you can still evolve teamates.

The Final Mission: The Hunt for Darkrai![edit]

You'll have to talk to Ursaring in Treasure Town, and you'll gain access to Mystic Forest!

  • Mystifying Forest
  • Difficulty: 10
  • Boss: The Guild (8)
  • Floors: 13 + Interior
  • Notes: Pokémon are randomly placed on the floors

This dungeon can be a pain. You just have to be lucky and get a right list of Pokémon in this dungeon. After 13 Floors, you'll meet the Guild.

  • Wigglytuff
  • HP: 800+
  • Normal
  • Average Damage: 20+
  • Chatot
  • HP: 300+
  • Normal/ Flying
  • Average Damage: 20+
  • Others
  • HP: 100+ apiece
  • Varies
  • Average Damage: 10+

This fight can be intense, especially due to the fact that you can only bring you and your partner. First, look downward and unleash a Long Range attack, if you don't have one of those use a throwing item, to land a little damage. Then if you have a Character Range attack like Lava Plume, start punishing them with that. Eventually, they'll falter.

The Guild will run off, leaving you to continue your business. You'll follow Teddiursa and Ursaring to a spring. It'll start to light up in the middle, and Teddiursa will step in, and evolve into an Ursaring. Then your partner will go in, and it'll say that it can't. Oh well, just come back later, since now, the Guild has something waiting for you!

When you get back to the Guild, they'll surround you and cheer for you. You have become an advanced Exploration team, and it's time you moved out. But, they'll give you a few items, an extra space in your toolbox, and 10,000 Poke as a going away gift!

You'll find residence in Grovyle's old hideout, and that'll be your new team base! However, you can still go into the Guild to pick up missions and stuff!

You now have access to more dungeons, including the really long Zero Island series of dungeons!

Next thing you have to do is talk to a Mr. Mime outside of the Kecleon Shops about a missing Scizor, and you'll gain access to Blizzard Island! However, if you want to, you can recruit some Legendary Pokémon! See Pokémon Mystery Dungeon: Explorers of Time and Explorers of Darkness/Legendary Pokémon|Legendary Pokémon for more info.

  • Blizzard Island
  • Difficulty: 9
  • Boss: None
  • Floors: 20
  • Notes: Pokémon are randomly placed on the floors.

This dungeon is a real pain, even if you're a Fire-Type. If you have Dialga on your team, use it has the Leader. If you don't have Dialga, refer to the Legendary Pokémon guide up above. After 20 floors, you'll hit the bottom of the dungeon.

You'll now have a straight shot at the next dungeon now, Crevice Cave. But you can go back to town first, if you want to.

  • Crevice Cave
  • Difficulty: 8.5
  • Boss: Froslass
  • Floors: 10 + 14 + Bottom
  • Enigma Legendary Pokémon: Darkrai

This dungeon isn't as hard as the last one, but, as usual, should still be treated the same. Just keep going, and use the save point, if you have to.

After a little more, you'll reach the boss.

  • Froslass
  • HP: 950+
  • Ice/ Ghost
  • Average Damage: 10+

This is by far one of the easiest bosses ever. Due to its type matchup, it has a ton of weaknesses. They are as follows:

  • Fire
  • Rock
  • Ghost
  • Dark
  • Steel

So if you did take a Dialga, like you were told to, you shouldn't have a problem. Just keep pounding on her with Metal Claw, AncientPower, etc., until she finally faints. If you don't have Dialga, just pound it with attacks like Ember, Rock Throw, etc.

You'll notice that Scizor is trapped in a block of ice, you'll save it, and you did it!

Now that you did all of that, you can now enter Event Dungeons! Go to the event dungeons to learn more.

Do a few optional Missions, and then talk to Sunflora near Croagunk's store in the Wigglytuff Guild to get a mission to retrieve a Manaphy egg.

  • Surrounded Sea
  • Difficulty: 7
  • Boss: None
  • Floors: 20
  • Notes: Pokémon are randomly placed on floors
  • Enigma Legendary Pokémon: Lugia

This dungeon is a major break from the last. Just keep going, and you'll reach the end. If you listened to the tip about Shinx and got a Luxray out of it in Chapter 10, use it as leader. It'll take out anything in here, even if it's Lv.35. Eventually, you'll reach the bottom.

There will be 3 treasure chests, and you'll get to pick up all of them. Then if you go up a little bit, you'll see a weird Egg-looking thing. Pick it up, and leave the dungeon.

The next day you'll notice the egg hatching, and out will pop a Manaphy! It doesn't join your team yet, but you have a Manaphy! You'll take it to Sunflora in the Wigglytuff Guild, and it'll start crying. You'll have to get a Blue Gummi. You'll probably find them around Water-themed levels. If you forget what the word for Blue Gummi is, then talk to your partner with R and look at the Yellow highlighted part. Chatot gives you advice on where to find Blue Gummis, though, if you have trouble. They can usually be found around Craggy Coast, though this can take a while, you do want to get further in the story, right? So go!

  • Craggy Coast (Revisited)
  • Difficulty: .005
  • Boss: None
  • Floors: 9

This dungeon should be way easy now, just keep going. Look around everywhere, there's no telling where they'll be, though they can be spotted around B7F, though, if that makes the search easier for you, although that is an unconfirmed statistic, so just keep your eyes peeled. Cover every last room, but you don't have to use the hallways if you don't want to. Be sure to pack some Apples, because otherwise you'll faint for sure.

After you give Manaphy the Gummi, it'll move in with you (But still not on your team) and ask for another Blue Gummi, but since you know where to go, it shouldn't be a problem!

  • Craggy Coast (Revisited)
  • Difficulty: .005
  • Boss: None
  • Floors: 9

This dungeon should be way easy now, just keep going. Look around everywhere, there's no telling where they'll be, though they can be spotted around B7F, though, if that makes the search easier for you, although that is an unconfirmed statistic, so just keep your eyes peeled. Cover every last room, but you don't have to use the hallways if you don't want to. Be sure to pack some Apples, because otherwise you'll faint for sure.

After giving the Blue Gummi to the Manaphy, you'll go to bed. When you wake up, Manaphy will want to visit the beach south of town. Go there, and a scene will occur. You'll fall asleep, and when you wake up you'll notice Manaphy's not in bed. You'll head out to look for Manaphy when Chatot will catch up to you. He'll tell you Manaphy's gone to the beach again, so go there. There, you'll find Manaphy has fallen ill. After a bit, you'll gain access to Miracle Sea!

  • Miracle Sea
  • Difficulty: 8
  • Boss: Gyarados
  • Floors: 18 + 4 + Bottom
  • Notes: Bring an Electric Type for the boss; will make things a lot easier.

This dungeon can be a bit of a pain. The Sharpedos here will make getting through this dungeon really hard, even for Grass Types, so keep a lookout for those. There's a Save Point in the middle, so use that if you feel you should. After an accumulated 22 floors, you'll reach the boss.

  • Gyarados
  • HP: 1200+
  • Water/Flying
  • Average Damage: 20+

This boss is too easy, especially if you brought an Electric Type like Pikachu or Luxray, but if you didn't, you shouldn't have too much a problem anyway. Just keep pounding it with either Elecric or strong attacks, and you should bring it down.

The Phiones here will give you the water you were looking for, so with that in hand, you'll leave.

You'll give Manaphy the water, it'll wake up all better, and everybody'll be happy. However, now a Walrein has come to take it back out to sea where it belongs. Everybody will cry, but not stop Manaphy from leaving. You're probably miffed that Manaphy didn't join your team, huh? It will, don't worry.

Also, if you want to, if you return to Miracle Sea you can recruit Phione automatically!

Now, just keep doing optional missions, and after about 2 go downstairs in the Wigglytuff Guild to the floor where your room used to be, and a scene will occur involving Medicham, Gardevoir, and Lopunny of Team Charms will want an escort to Aegis Cave. Since nobody will do it(And since you're so special), you'll go with them.

  • Aegis Cave
  • Difficulty: 4
  • Bosses: Regice in Regice's Chamber, Regirock in Regirock's Chamber, Registeel in Registeel's Chamber, and 4 Hitmonlee, 4 Bronzong and Regigigas in Regigigas' Chamber
  • Floors: 3 + Regice's Chamber + 3 + Regirock's Chamber + 4 + Registeel's Chamber + 5 + Regigigas' Chamber (19 in total)
  • Notes: Bring Fighting Type for all the bosses; Dialga would be good for Final Boss.
  • Enigma Legendary Pokémon: Mewtwo

This dungeon isn't hard as much as it is long. It might take you 30 minutes to get through it! What you have to do is find the correct Unown Stones and put them on slates in Midpoint areas. However, you start out in a Midpoint area, but you need the Unown Stones! If you read the Slate, you'll notice that it says ICE somewhere around the writing. Go find the Unowns that match that. This is the long part. You have to find Unowns I, C, and E, defeat them, hope they drop a bluish rock, and pick it up. In total, you'll need the following stones:

  • C: 2
  • E: 3
  • I: 1
  • K: 1
  • L: 1
  • O: 1
  • R: 1
  • S: 1
  • T: 1

Knowing that, if you see any you think you don't need, think about it! You may need doubles, or even triples. Anyway, after collecting the three letters, return to the Slate Room and put them in. If you didn't collect them all, go back through. After you put the stones in, the Slate will glow, vibrate, etc., and then break. Under it was some stairs. Go under when you think you're ready, and fight the first boss, Regice.

  • Regice
  • HP: 600+
  • Ice
  • Average Damage: 10+

This isn't hard at all, just go back down a space to get with your team, and wait, and start pounding it with attacks. It really isn't that hard. If you brought the Fighting Type with you, use that. After you're done, the lead character will be endowed with Regice' power and break a wall. Now your team will go through.

Now you need to collect R, O, C, and K. Go through the 3-Floors Maze, and when you get those, use them on the Slate, and stairs will appear. Go down and fight Regirock.

  • Regirock
  • HP: 600+
  • Rock
  • Average Damage: 10+

This isn't hard either, especially with a Fighting Type. If you're starting to notice a trend here, you're not mistaken; all the bosses here are weak against Fighting. Just do what you did with Regice, and go through.

Now you need to find the letters S, T, two E's, and L in the maze. Once you get those, fight the next boss, Registeel.

  • Registeel
  • HP: 600+
  • Steel
  • Average Damage: 10+

Same drill as the other two. Just back up and pound on him when he gets close. Eventually, he'll falter.

Now you'll enter a maze, but thankfully, you don't need to actually find anything. Just get through the 5 floors, and meet the boss. Thankfully, you fight them all with Team Charms.

  • Regigigas
  • HP: 1500+
  • Normal
  • Average Damage: 30+
  • Notes: Moves 1/2 speed for first few turns.
  • Hitmonlee (4)
  • HP: 100+ each
  • Fighting
  • Average Damage: 20+
  • Bronzong (4)
  • HP: 100+ each
  • Steel/ Psychic
  • Average Damage: 20+

This fight is a little hard, but if you brought a Dialga, the problem will be gone. If you get Dialga to use Roar of Time on the first turn, then just about all of them will faint, leaving only Regigigas to try to beat you. Regigigas moves once for every 2 times you move for the first few turns because of its Slow Start, so use that time to pack in some damage. If you brought the Fighting Type, get it to attack Regigigas. Eventually, it'll faint.

The team will cheer, until Regigigas gets back up and starts running after you. You all will run away, but as you do, you'll notice a new dungeon, Hidden Ruins. The only significance of the dungeon, though, is for hold items for the Regis.

There is a cut-scene in the latter days, revealing Darkrai and Cresselia. Darkrai reveals his lust for darkness, while Cresselia tries to do the right thing for justice. You will then have a visitor in your dreams. This visitor is Cresselia. She'll tell you that your existence is breaking the fabric of space. Continue on through the days and you'll get more info on your "destructive habits." Eventually, you will be informed in the beginning of the day that Azurill is in a deep slumber. The only way to help him is to find Drowzee, who; informed by Magnemite, has stopped his ways of crime. He is on Mt. Travail.

  • Mt. Travail
  • Difficulty: 8.5
  • Floors - 19
  • Boss: None

This is a very hard dungeon. There are a lot of very strong Pokémon, like Scizor and Kangaskhan. If you do need experience, though, this is the place. Most of the Pokémon in this dungeon will give you 500-600 Exp. when you defeat them. When you face an enemy in this place, ambush him/her. Make sure you bring items just in case you find an unfortunate Monster House.

When you have reached the peak, Drowzee will suspect something. Then, your partner says to him that Azurill is having a nightmare. Eventually, he'll help Azurill.

  • The Nightmare
  • Difficulty: 7
  • Floors - 17
  • Boss: None

This is actually pretty easy. Be wary for Chansey and Blissey, for they give you 1000+ Exp.! Not all the Pokémon are evolved, so this dungeon should be pretty easy.

At the end of the dungeon there is Cresselia, poised to kill you. Before she does, Pikachu comments, "Your'e the one in my dreams!" or something like that. Drowzee waddles in just as Cresselia disappears. He brings you out. The next day Pikachu decides to ask Lapras about the whole distortion of space thing. Lapras doesn't know much except that there is "one being that embodies space itself. Its name is Palkia. It dwells in a place called Spacial Rift." Lapras doesn't know where Spacial Rift is. That night where all is quiet and asleep. A rumble in Sharpedo Bluff wakes you and Pikachu. Palkia flies in and takes you to Spacial Rift. Which is on the other side of the continent. He is ready to kill you saying stuff like "You dare to distort space! I will not allow it!" He backs you up to the nothingness behind you and you fall to the entrance to the dungeon.

  • Spacial Rift
  • Difficulty: 8.5
  • Floors - 15, 9
  • Boss: Palkia

This place can be hard if you are not well trained and or have next to nothing in your storage. Don't go easy on any of the Pokémon. Especially Gligar who knows Guillotine. After what seems like pure heck you have Palkia, who only has one weakness, Dragon. Use all your neutral moves and he should go down. Be wary of his Spacial Rend, that doesn't need recharging like Roar of Time. After that he freezes and some outside voice tells you to go into Palkia's dream.

  • Palkia's Dream

You and your partner enter Palkia's dream. Invaded, Palkia tries to flush you out.