I dunno how "extremely" obscure it is, but I haven't heard anyone talk about it in years, and I have a big soft spot for it so I'll shout it out whenever I can.
Shadow Watch is an X-Com clone, but with a heavier emphasis on story (based off of a Tom Clancy novel), and a permanent team as opposed to the generated soldiers of X-Com. Your team of six consists of multiple specialists, from a sniper, to a demolition expert, and you have to pick and choose your team based on mission type and map layout. There are your given assault "destroy everything" maps, but there's also infiltration, kidnapping, defense missions and more depending on your choices.
Oh yes, the choices. Shadow Watch has 3 chapters, taking place in different locales around the globe. Which one you go to initially is chosen at random on every playthrough, and in addition to each locale having a couple set starting plot points that it also cycles through every playthrough, your experience and missions will change rapidly depending on how you interact with your contacts between missions. You can take different sides in conflicts, or have your decisions in one area impact your available missions in the next area. Being 9 or 10 at the time, having the game feel reactionary to how I played blew my mind.
Aesthetically the game has a pretty unique style, too. The comic-book style portraits, the almost cel-shaded look of the models in-game, the
soundtrack composed by Bill Brown, all of it combines for a really unique experience. I loved Shadow Watch, and it still hold up well, and I'm sad it never got the recognition I thought it deserved then or now.