I think it'll be a new story, sorta like it'll have links to the first one, but new characters and stuff.
Maybe somthing like this:
You were one of the black ops in the Black Mesa accident but you were dis-honorably discharged after they found out you had a chance to kill Gordan Freeman but you didn't. Anyways you get a new job and 5 years pass, but suddenly portals start opening up all over the world, and Aliens from Xen start there attack. They do massive damage to the world, and you are forced to take up arms and help destroy the Aliens. You head to a military base to get weapons and armor, but then you come across the body of Gordan Freeman who appears to be frozen in a some type of stasis cell. Just as you goto leave the room a portal appears and lightning fires out at you and you are knocked back, a little friend called Alien Slaves jumps out of the portal, yet he is different, bigger, and more powerful. You get in a fire fight with the alien, but your bullets and grenades do nothing to him. He backhands you and you go unconcious. When you ifnally wake up Gordan's body is gone, and so is the alien.
Or somthing like that. Then, well you can tie in alot of informaiton which wsas left open in the first one, and still keep asking questions, like why did they keep his body, and why did the alien take it.