Very, very, very few games are non-linear. Some (like Deus Ex) have story trees, but you do all the same things, then you have a choice, then you get back onto the track. Most of the time, non-linearity in games doesn't work very well, because the player will feel lost/get killed, and the story won't play out properly. Really, non-linearity is overrated, but story trees are underused.