Its not like a really obvious story.. all the little scenes just set the tone, as time wears on and fewer and fewer other people appear before finally Black Mesa is totally empty of surviving humans except for you, some soldiers, and the G-Man. I get the feeling that HL2 kind of retrofit a story back in HL1.
The Combine came after you killed the Nihilanth at the end of the first one. The green lightning shooting aliens were slaves of Nihilanth and you freed them, so they are now on your side. The rest of Nihilanth's aliens had fled from the Combine and were followed by them through the portal to Earth.
If you want to fill out the story more, read Wikipedia. There is a lot of information in there that is very (Very very very) easy to miss while actually playing through the game, and then some additional info that was not in the game.
Even though its not a story like, say, Metal Gear Solid 3, I still get totally engrossed in it... for instance
| At the start of Episode 2, when the Hunter appears for the first time and you are trying to get away, and then it totally fucks up Alyx right in front of you, I couldn't help but shout "noooooo!!" (with sudden sincere despair) Same thing at the end with Eli. |
I felt like a geek but still, that is a standout moment in gaming for me right there. Catharsis, man, catharsis..