When you complete any random missions after graduating from the guild in Pokemon Mystery Dungeon, you can go down into the lowest floor of the guild and you will meet team charm, from the special episode. You go with them to Aegis Cave, where you have to gather Unown stones to proceed and fight the bosses Regirock, Regice, Registeel and Regigigas. The bosses only seem to appear the first time you go to the cave, though.
From Neonspectre
Mewtwo isn't at the end of a dungeon in pmd2 so you need to have a secret stone slab or mystery part and go to dark crater B6 or Aigus cave deepest part B5 Mewtwo is only found in DARKNESS if you have time and don't have any friends with darkness, your out of luck! if you need a mystery part or secret slab here are some wondermail to get it: Y%PQ 8X0& 640N (mystery part) +#X0 0CN6 7&49 JF4K %@%9 2H34 (secret slab) TP24 4T=% X=-=
you go to surrounded sea. first to unlock it you have to talk to sunflora. and then..... voila it unlocks! then get the egg at the end of the dungeon and a Manaphy hatches from it! yay!!! then you unlock miracle sea because Manaphy is sick.... THEN AFTER THAT you recruit manaphy after the Darkrai mission AND THEN you can recruit the legendary pokemon: Zapdos,mewtwo(dark version only) Celebi(Time version only),Raikou,Entei,Lugia,Ho-oh,Latias,Latios,Deoxys,Darkrai(a DIFFERENT Darkrai) all with a special item called the Mystery Part/Secret Slab! HOORAY FOR LEGENDARY ITEMS!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!