This game is much less linear than most Nancy Drew games. That is, while some events will trigger other events, you can follow many different paths to get to the end of the game. Feel free to follow whatever interests you the most; you can, for example, completely repair both the large and small Tesla coils before you get the audio player on Niko's desk fixed.
For this reason, I've grouped the puzzles by the place in which they occur. If you can't find what you're looking for in the place you expect to find it, check out the section titled "Puzzles," where you'll find every puzzle in the game listed. I don't recommend you start there, however; you may see puzzles you don't know exist and you'd rather discover for yourself, so approach with caution.