My top game stories are Silent Hill 2, Tactics Ogre: LUCT, Grim Fandango, Suikoden 2/3, and Killer 7.
In my personal opinion of course, Silent Hill 2 is the greatest video game story ever made. Lots of people might say Planescape but much of Planescape is text which could easily be done in print. Silent Hill 2 is unique in how it portrays its story via nothing but visuals, dialogue, and player choice. It’s a uniquely video game experience. Every enemy has a backstory and relevance to the plot and contain their own layer of symbolism and this goes beyond Pyramid Head. The fact that the ending changes depending on what you do in-game, such as going to the menu a lot or checking the letter a lot, the multiple endings, and the level of player interaction make Silent Hill 2 ascend to the greats of the medium that is presented in a way that only a video game could articulate. This is without touching the messages, subtext, symbolism, and themes contained within it.