The plot is just a pretense to justify going out and killing things, so you can get better equipment, so you can kill stronger opponents, so you can get better equipment, etc. Pretty much any evil characters (aliens, robots, etc) could be swapped in without a huge impact on the game, other than atmosphere / style (though I got bored with both games and didn't finish either).
Most of the actual story was told in cutscenes, which were quite well done.
