Zero Escape: The Nonary Games

Files are usually found in VLR's escape rooms, though you will also get some via natural story progression. Generally the files you pick up in the escape rooms are clues used to solve the puzzles in each room. As long as you're searching the escape rooms and not just doing the bare minimum needed to get out of the room, you don't need to worry about this trophy.

On the flowchart, you can check each escape room once you've cleared it, and you will see "Archives" followed by a number (X/X). As long as the two numbers add up, you don't have to worry about a thing (this number also counts the secrets folder in each room [see Redacted]). If you're missing something, go back into the escape room and pick up whatever you've missed. Once you've picked up the missing item, you can leave the escape room either by opening the safe and leaving or simply going back to the flowchart.