Glad to see you enjoyed the game! The theme was added by leaving the safe areas to progress. Also in the second ending the theme is added because you have to leave Clack behind. Also the world can be easily explored if you start collecting upgrades (light blue objects). Exploring the world will reward you nicely 😛
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To add the how the theme was implemented the original way we planned to implement the theme was by using oxygen as a propellant and leaving it behind to explore the area. We quickly figured out that the theme wasn't strong enough so we added the narrator so that in the ending you had to leave him behind. A voice is missing for the final area where he says "I guess you have to leave me because there is no way to save me." This was discovered after the jam had ended and I felt that since it wasn't game breaking it did not need fixing.