Parasite Eve.
Literally the definition of lightning in a bottle:
- Smooth active time combat
- Modern (as of 1997) setting in New York with an interesting twist on its sci-fi story (hard enough to be based on actual science, but soft enough to allow a lot of cool crazy shit to happen)
- Very linear admittedly (unless you go into the Chrysler Building), but the environments have a lot of atmosphere and a lot of presence to them
-Hot, smart, cool and deadly female protagonist Aya Brea and your typical 90s diverse cast (who come off as actual people rather than props for the protagonist to play off of)
Minor spoiler: A really funny racist joke when Maeda is introduced
-Amazing soundtrack by Yoko Shimomura and a great ending theme
The sequels definitely didn't do it justice. PE2 was just Resident Evil but replace the T-Virus with mitochondria. It's a rather good but generic survival horror game of the time with some RPG mechanics slapped on. Not a bad game per se (it's a decent game to play for the ~10-20 hours it lasts), but not amazing like the first game. The third game has a horrific story but the actual gameplay is okay. Also they make Aya an annoying helpless woman when that's the exact opposite of what she is in the previous two games. Some people were bitching about sexism when it came out and while I won't go that far, they really aborted her character and just made her into a lame sex object for the director to project his fantasies onto (as she takes damage her clothes become more ripped up. Nothing too bad but still...).
The only game I think counts as a sequel of sorts to Parasite Eve is vagrant Story and I haven't finished that one yet. It uses the same battle system as Parasite Eve but more advanced and the game is a marvel to look at in addition to playing. Plus, it's one of Squaresoft's last games before becoming Square Enix, so I see it being the only true sequel to PE.