I have begun integrating the bacteria and player ship into the game over the past few days. The player ship will be able to interact with the various forms of bacteria in each level. The design aspect here is to be able to require the player to think strategically and get the hydrogen produced instead of trying to do everything on his/her own. I still want the level design to leave things open to the interpretation of the player, but make them think about what is going on.
Oh well, more on the design when I get back!