I"m gonna assume that spoiling a storyline from a 1998 game is allright, if you haven't played the game by now and want to know its story I don't think its warrentted to use the spoiler tags.
Basically as I recall you beat the final boss and free the voritgants from slavery , and the FBI dude offers you a job with them.
The thing you really dont' find out is what happens between teh first and second game , they cut most of that stuff from the half life 2 storyline.
Basically the alien race that was behind the scenes in half life 1 invades the earth through one way portals , and the stuff that happened at black mesa is happening all over the world , people start to take refuge in the bigger cities , then these alien citedels appear and armed combine troops basically take over earth. It's also alluded that these aliens are stealing earths water supply , that's why all the shorelines you find in the game have old beached ships, and assumably also what those giant oil derrik like machines are for. So basically you get sent to fight off the combine and assumably save earth.