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The Mystery of the Nautilus Hints
Try things repeatedly
Not everything "works" the first time. There are a number of actions, puzzles, etc. that are only accessible after some other event has happened. If you have tried something that you think should work (but didn't), try it again after you have encountered some other circumstance, visited some other place, met some other person, or obtained some other object.
Also, the nature of the game often requires that you perform certain tasks which, at the moment, may seem totally unrelated to what you are working on, but which -- due to the design of the game -- must be accomplished in a fixed order before you can progress. The best suggestion is to try to do everything possible in every location you are in, and not just limit yourself to attempting to solve one puzzle at a time.