I had this idea for doing something myself... It was something like this:
The player (Gordon, for me) is sent for a sample of some biological stuff to a little lab outside the city, surrounded by forests and a river that goes into the city... As he is reaching for it, armed forces take out the lab and looking for the sample themselves, taking it somewhere in large trucks (in their way they have killed much scientists, of course). The player has to get out the lab avoiding contact with armed forces (as he ain?t armed at first) until he finally comes out to see the trucks heading to the city.
Armed and dangerous :P, the player gets a jeep (maybe with some Barney) and chases the trucks (little scripting). While the vehicles are racing, a struggle takes place (func_conveyor) where the player is able to assault the truck and steal the sample (as soon as the player leaves the jeep it?s destroyed)... The whole convoy is destroyed by accident and a hurt player must get through the forest and river to the city while the armed forces look for him. Once he gets to the city he must take the sample to a scientist in an appointed building but the city is being attacked by... Aliens!!!. Of course, armed forces are also fighting there...
Well, the player takes the sample as he can and the he gets instructions to take it to a manor in the oldest part of the city, where a secret lab is, in order to stop the alien thing. The player crosses the city, gets to the manor and well... It keeps on going but basically he stops the invasion and has to scape the place...
Boring?.