Puzzle 0: When you hear the alien nearby, hide. When you hear the alien in the distance, move cautiously. When you hear the alien kill someone, run.
Puzzle 1: Pour the right bucket into the small bucket (3, 1, 3). Pour the small bucket into the left bucket (6, 1, 0). Pour the right bucket into the small bucket (6, 0, 1). Pour the left bucket into the right bucket (2, 4, 1). Pour the right bucket into the small bucket (2, 2, 3).
If the guard responds well to "Hey, man, how is your shift going?": "These guard-duty shifts can be so long. You must be looking forward to taking a break." -> "Say, do you want me to take over for you?"
If the guard responds well to "General wants to see you.": "He didn't say why, but it sounded urgent." -> "I don't ask the General questions and neither should you."
If the guard responds well to "The mess is on fire!": "There was a mishap with a toaster and the whole kitchen went up. Lotta grease in there, you know." -> "It's out of control! We need all the manpower we can get!"
Puzzle 4: Charity is the saboteur. Her shoe size is 8 and she was wearing black.
Puzzle 5: Fill the large bucket (9, 0). Pour into the small bucket (5, 4). Empty the small bucket (5, 0). Pour from the large bucket into the small bucket (1, 4). Empty the small bucket (1, 0). Pour from the large bucket into the small bucket (0, 1). Fill the large bucket (9, 1). Pour from the large bucket into the small bucket (6, 4).
Puzzle 6: Ask the kids for help with the bakery. Ask the annoyed woman for help with the men's accessories salesman. Ask the cattle merchant for help with the ceramics. The password is SUPER STAR.
Puzzle 11: This one's a fakeout. After four moves the protagonist will find a more creative solution, no matter what you do.
Puzzle 12: The first cipher is an unshifted Polybius square that resolves to "PASSWORD." The second is a Polybius square with the keyword(s) "ACID BURN", which resolves to "TO THE STARS".