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This is a "dark horse" entry, but I believe that the FPS Marathon by Bungie Studios made the biggest leap. While it clearly owed a great deal to Wolfenstein and Doom, Bungie forked off the path from the iD model of FPS design by giving the player a quiet, almost poetic atmosphere of dread and anticipation and including a backstory and narrative that gave you other reasons to explore besides gore and destruction. Using advanced (for the time) lighting, smart AI and a much slower pace, the game was all about atmosphere; the first few fights you have are among the most intense I've ever experienced. No heavy-metal guitars, no chainsaw, just you and a half-clip of pistol ammo and a dark, utterly foreign alien-ship corridor; the sensation of being truly alone made you yearn for the next data terminal, where you would log in and receive tiny, enigmatic pieces of a story that pointed to a greater whole.
Marathon also innovated in multiplayer to great effect, with King of the Hill and other tactics-inspired combat modes and some truly hilarious physics as a result of grenade or rocket hits. Long before Half-Life 2 allowed me to kill someone with a toilet, Marathon perfected launching opponents into the lava with a well-placed rocket between the feet -- instant comedy gold. The weapon balance was also superb; each weapon's power was balanced out by a negative, such as the intimidating rocket launcher that only held two rockets and had enough of a "kick" to throw off your second shot, should you linger on the fire button.
I suspect the submissions for this QOW will be inundated by Half-Life and Halo nominations, but Marathon players such as myself can smirk quietly knowing that Bungie's Marathon was the proving grounds in which they tested almost every element that made Halo what it is today (vehicles excepted, of course) and innovated in storytelling and atmosphere long before Gordon dodged his first headcrab. You had to be initiated into the cult of Macintosh to play, but that's what makes Marathon such a rare pleasure.
-Michael Eilers, University of Advancing Technology
Deus Ex was more than just a first person shooter. It made you part of a believable future where conspiracies lay hidden around every corner waiting to be uncovered. Deus Ex made big strides not technologically, but more from a design point of view.
It gave birth to emergent gameplay, it changed the way at least the way I think games should be designed. It puts the player in a situation and the player should act as they please, but they will also have to accept the consequences of their actions. Deus Ex isn't like Half-Life or some other boring first person shooters because there's not one way (there's infinite solutions to problems, like in real life), you don't play the game as the designer intended you to play it, the designers encourage you to play the game with your own style, and the skill points and augmentations are used as tools to reach this goal. I think Deus Ex is a quantum leap from the likes of DOOM, and Half-Life, because it is believable, fun to play, it gives you variety, and it has a great epic story tying it all together.