As much as I'd like to recommend house-rules to provide for a "realistic gunfight" with the built-in cover-rules... I can't.
The problem with D&D in general, in light of this question, is that it promotes "heroic" games, where creatures routinely take (unless they're first level wizards) dozens of sword hits without being too much worse the wear. Your objectives are: sci-fi, realistic, very tactically, and interesting cover.
Let me address the points individually:
D&D can certainly do the more space-opera/fantasy style "sci-fi" settings, but you'll have to work to adapt the rules. I personally treasure my "Fading Suns" rulebook that provides an excellent treatment of a sci-fi 'verse with 3.0 rules. ... But I don't play it. It's probably worth shopping for a system that is designed around the setting you want to evoke.
Default 3.5 (not looking at modern here, cause I've got no experience with it) can't do gunfights worth an expletive. Default guns, those presented in the D&D DMG (and doing a quick google around, found here) ... don't do realistic damage. A .357 magnum, according to the wiki, does 2d12 damage. If you're getting shot for 2d12 damage, it certainly hurts, but there are better things to do than to seek cover.
The problem with the gun rules in 3.5 is... you'll be doing so much work houseruling them and finding good patches that you might as well find a better base system. Upping their lethalty is great, but then characters... don't feel like being heroes. Cause it hurts.
Cover in 3.5 is handled with a number of conditions, with very little to differentiate between things granting the same conditions. This is absolutely appropriate for the things being modeled in 3.5, especially considering that you generally don't want people using cover in a heroic game. It's just not fun.
The best cover-based game that I know of is Aces & Eights. Where you have a shot clock, you apply the cover, physically, to the clock, and then you see where you hit. It's also the most realistic. It would take a bit of effort to adapt the shot-clock to an online setting though.
To sum up, D&D is designed for heroic melee combat. Tactical cover based shooting is a stretch that isn't supported particularly well. While it's possible to do so, and I support @MadMAxJr's answer in that regard (especially regarding the massive damage), keeping track of the house rules will be difficult and frustrating.
I encourage you to post a new question (if you think my answer has merit) with details of your setting, soliciting systems. (I'm having a hard time of thinking of any to recommend that are non-generic off the top of my head.) Barring that, explore what GURPS has to offer, as that system can tend far more to the realistic than D&D.