This guide contains some minor spoilers. If you want to play through this game completely unspoiled but still worry about missing some achievements, here’s what I would suggest:

1) Read about “Dough, Not Whole” achievement – it has to be done early in the game and is missable.

2) Vinegar you obtain early on is used for one of the achievements, so make sure you have a few spare bottles until you’ve got it!

3) Play through the game normally until you are about to return back to school. If you are still missing any achievements other than “Victory!” and “Thesis defense” at this point, refer to this guide: all achievements from early middle to late game can be obtained until the very end.

After you are reunited with Andrea, go to the junior school. After a short quest, Andrea will clear out the slime allowing you to get to junior school. There search the rooms – in one of the rooms Andrea will find a box of doughnuts, only to have them stolen by an alien pseudoplant. You will have to chase down and kill the pseudoplant – it will keep running away but you can usually put in a blow or few, so keep chasing it and it will eventually die, earning you this achievement.

Use Vinegar to kill Base Squelch. Vinegar is obtained during aforementioned quest; you get a number of spare bottles after Andrea uses some to clear out the slime. Squelches of all kinds, including Base ones can be found in the swamp.

Pomelos are found in easily-missable hole on the very first map in the alien world.

Hairballs are found in the hole in the left passage right after you cross the swamp.

Alien seeds are found in the secret tunnel during the later portion of your adventures in the alien world. Simply explore the secret tunnel that Missy finds and check out the hole in the end of it.

You may miss the secret tunnel itself if you fall into the pit yourself, but in this case going back into the tunnels and exploring them should still trigger the scene where Missy finds it. If you don’t fall into the pit (i.e. if the main character is early in party’s movement order), Missy should automatically find the secret tunnel on the way out. (This might sound a little confusing if you haven’t reached that part yet, but once you are there you’ll get what I mean ^_^; )

You have to win the game, duh.

You have to win the game on highest “Graduate” difficulty. It isn’t that hard, actually, so you might as well start playing on it off the bat. Note that you can't change difficulty in the process, so if you started playing on lower difficulty but then decided you can handle "Graduate", you will have to start anew.