Well, number 3 is coming out, and the first game is getting a remake, but what about the game that sits in between the two?
System Shock 2 was released in 1999, which put it up against the original Half-Life. While critics praised it, it was heavily overshadowed by this other FPS, leading to it never escalating beyond cult hit status during its normal sales run. However, its influence goes well beyond that.
This game has been wide touted as one of the scariest games ever made. The thing to realize here is that it relies on a different brand of scariness than modern horror games, which make heavy use of jumpscares and extremely limited lighting to freak the player out at specific points.
2 leans more on a sense of overall tension; while the enemies aren't that scary (at least, not unless you stop and think about what they are), the music, atmosphere, and limited resources put players constantly on edge, with limited breathing room. Of course, the reason this isn't popular is that it's too easy (by some views) to paint yourself into a corner by using too much ammo or healing items. The difficulty (which was fairly hard, even by standards back then) did not help matters.
While it took years for an official sequel, many games were influenced by it. The Bioshock series began as a direct spiritual sequel to the game, and circumstantial evidence indicates that the first Dead Space game may have started development as a sequel. More directly, it helped blend the FPS and RPG genres, in a way that would be echoed (although not copied) by later series like Borderlands.
Oh, and SHODAN. Many, many video game AIs have taken cues from SHODAN and her brand of insanity. From Halo's Cortana to Portal's GLaDOS (note the use of capital letters) to Angel from the aforementioned Borderlands, female AIs have become surprisingly standard since this game's release. A trope, if you will, that goes back to "L-l-look at you, hacker..."
The final coda is the legal rights snafu that was the main reason it took so long for ''3'' to come out, due to the rights being divided among several different companies. Trying to sum up just how those rights were divided over the years would be very complicated, so I'll settle for just saying that the sequel rights, the distribution rights, and the trademark rights have changed hands multiple times. (At least it's in a better position than No One Lives Forever...)
Either way, it's another piece of gaming history that deserves to be highlighted. SHODAN's glory may not quite be what she wants, but in terms of being the center of a memorable game, she's earned a fair amount of respect, right?
Oh, no one asked you, Goggles.