The best story line in a video game series is without a single doubt, the Halo trilogy. Many people that have only played Halo 3 and haven't bothered with the campaign in the first two look by this, and say things like "wtf Cushion Halo 3 didn't make sense!!!!" (Probably because you didn't beat the first two jackass)
Halo is very in depth, and it even has novels adding even more depth to the storyline (Fall of Reach, The Flood, The First Strike, Ghosts of Onyx, Contact Harvest)
What other game could beat that? Call of Duty? GTA? Rainbow Six? *** that! If there was an award for best video game storyline, the Halo series would take it no questions asked.
Must...listen...to more....metal!