Pokémon Super Mystery Dungeon/Chapter 3

School
Nuzleaf will lead you to school before introducing you to the principal (Simipour) (and the grumpy Vice Principal Watchog). He then sees himself out before the kids start arriving. The principal introduces you to the other kids (much to their shock). An earthquake will then occur before you realize, that's your "partner" and he just "inflicted mortal pain" on your head. After he apologizes for crashing into you (and knocking you out), you pass out.

You then wake up in the school nurse's office (Audino) and she tells you to rejoin the class when you are ready. Exit through the southern entrance to rejoin the class (which is being taught by Farfetched at the moment). The other kids welcome you back and Farfetched starts yelling at them to sit down. Class continues normally until the end of school.

After school, your partner offers to show you a really nice place in the village. You and your partner run back through the path before Pancham and Shelmet stop you and offer to show you an even scarier dungeon than yesterday's dungeon (it's not that scary, so don't worry). Save and continue.

Drilbur Coal Mine
This dungeon is particularly easy to clear compared to the later dungeon, Poliwhirl River. It has a few fire types (which should be easy for you to take out if you chose a water type partner). It also has a mildly annoying enemy called Numel, who is resistant to thunder types. Although, it does take extra damage from Water types due to being a Fire and Ground type, so keep that in mind. There's also quite a few Rock types which should be easy to take out. The dungeon has 7 floors, with a rest stop on Floor 4. When you reach Floor 4, restock your Tiny Reviver Seeds and Oran Berries, then continue.

BOSS: Gabite
When you reach the final floor, you will hear some grumbling, and then the first boss battle will commence!

This boss is fairly easy to beat. All you have to do is use your Blast Seeds on him twice and he dies. After which, he will show you his treasure. Not that you get any, of course. After a couple of cutscenes, you end up on a hill with a tree, where you end up falling asleep

Later that night, you start thinking about why you turned into a Pokémon. Eventually, you go back to sleep. After that, it shows a cutscene of Rayquaza flying away, clearly running from something.