On the other hand, I reckon the raw free-form game-play would provide more emotive impact than the over-complicated plot that didn’t make much sense. Having the game-play as is would provide provide even more of an emotional bond, because the player would be able to assist and implement different environmental features for the lifeforms. And because the protagonist no longer exists the planet would more reflect the player’s own creative work. Having visual scenes of natural landscapes as the incentive for not purging the planet of organic life, could provide for more philosophic thought. In my plot the player is incredibly detached from the environment that they create. Gradual development of the planet gives a bit more time for player to ponder. I forgot to mention, eventually the planet should develop civilization and have civilization effect the fragile atmosphere (destroy it for their own means).
Another thing to have instead would be to just have a computer assistant rather than a human companion trying to change your opinion.
Whilst working through the plot a bit further, I decided to drop plot and back-story from the idea.
The goal of the game-play is to spark reflection on environmental effects from a larger scale, using an emotional bond of creation. The tag-line of this game shall be, “In order to create something, you must destroy something else.”