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The first-person shooter genre has never really been known for its rich storytelling tradition. Only in the recent generation has it become necessary to make up some manner of plot to give rhyme and reason to the endless slaughtering of monsters, aliens, and occasionally Germans.
Even then, many of the FPS games in the recent generation have tried very hard to incorporate it, and many times the offering is as laughable like Evil Dead (God bless Bruce Campbell). Every now and then, however, a blood n' guts shooter will feature a very surpisingly good storyline. Here are the best of them. Why seven? Why not!
7. Halo
The Halo series contains a rich, in-depth science fiction offering, telling the tale of a trained from birth, physically augmented super soldier named Jonn 117, or the Master Chief. The story is good, but it gets ranked last because you don't really get much of it in the games; you have to read the novels and other supplementary material.
6. Deus Ex
Another game with a very interesting in depth story. You play a nano-augmented anti-terrorist agent who is under the control of oppressive government posing as the good guys. As the story progresses, the lines become blurred and the people you killed early on are now your allies. The story takes you through all manner of locales across the world, and the characters are, for the most part, realistic.
5. Call of Duty 4
Often times war games will take the historic ground, telling something about WWII or something. CoD4 told a hypothetical story set in present day. It, of course, goes by the present-day applicable terrorism angle, where you play various characters trying to stop madmen from creating chaos in the world. It provided some of the most intesne moments in gaming; moments that shake the player to the core.
4. Bioshock (System Shock story was great also)
2K's anarchy beneath the sea was simply wonderful. The art-deco, the haunting music, and the troubling story of a city run mad with genetic experimentation, still ruled by the visionary dictator who had created the city in the first place. Through diary recordings you pick up as you go, you hear about some of the population and even seedy undercurrent of the city, various individuals struggling for control. Good twists, interesting characters.
3. Call of Cthulhu: Dark Corners of the Earth
Any Lovecraftian offering that binds itself to the mythos is bound to be excellent. Headfirst Productions provided a blend of a few of the stories, particularly focusing on the creepy isolationist town featured in "Shadows of Innsmouth." While it was as much as a puzzle game as a shooter (and the blend was not always very successful), the story was unsettling, creepy, and wonderful.
2. Half-Life 2
Valve's post-apocalyptic Orwellian love muffin features a rich and detailed story. Half-Life had become insanely popular do to its real-time cinematics, which never broke the flow of the game, but instead put you in the front seat running around when things exploded around you. The game takes you all over the place; there's love, loss, freedom, and heroism.
1. Marathon
Mac gamers have always been kind of an oxy moron, as it wasn't terribly often that a great game was made for the computer, much less exclusively. Most people haven't really heard of Marathon, and if you have, it's only based upon a general familiarity that the company that made Halo (Bungie) put together this FPS trilogy about twelve years prior. This was during the Doom era, when there was no story to an FPS. Marathon changed that (although wasn't so widely played that it transformed the genre), putting in humor and intrigue throughout all of the hours of play. If you ever get a chance, the whole series is available for download, and you can get them to work on PC with a little effort.