Here's what I got from it. You start as a solider in the empire, fighting the freemen. (first time I heard that I thought, what are we, communists?) Then you realize the empire is all evil bastards when they say "let's level the freemen village!" You live happily in the forest until the empire comes, destroys your house, and steals trees. As the story continues you see the empire mining ore and harvesting electricty from lightning. I assume this all is needed for some superweapon or something. The last chapter's opening screen descibes the empires city as having thin air, or someting. Then you see them planting stolen trees. You decide to blow up some trees or something so that the citizens of the city can't have any air, effectively doing the same as the empire did that made you rebel. (trees produce oxygen)
The story is confusing as hell.
Even if at any point it made sense it would still be pretty odd. I really hope I have no idea what the story was, because if what I said is right then it may be the worst story of all time.