Hrm. Actually, last night whilst playing, indeed, I finally found my first alien base (by this point, I was starting to wonder if there was supply ships but no bases). Went in, cleared it out with only 2 casualties (whole group is armed with coilguns so most battles aren't really problematic). And ... apparently that's game over!
From what i've seen on wiki, it looks like there's meant to be further plot-stuff already in-game (The Enemy On Earth, A New Twist, etc.) but I only ever could get as far as 'The Universal Serum'. Are these other researches and plot-stuffs in game already (and therefore I shouldn't touch any alien bases with a ten-foot pole so as to avoid game-end) or is that maybe only in latest version?