Intro
This idea is focused towards the Half Life universe but with a little adaptation could be used in other settings.

Insane?
The Prison guards are dragging you down the corridor. You are fighting as if you life depended on it. Suddenly there is a huge expolsion and the wall at the end of the corridor disintegrates and an alien slave walks through. He kills the two guards and then just turns away.

“Fools! I warned them this was coming but nobody would listen. The only way they could shut me up was to lock me in the Black Mesa Prison Area until after the experiments were over. Well, obviosuly my predictions were true. Just because I’m a janitor doesn’t mean I’m stupid! But why wasn’t I killed? Maybe the aliens are giving me a chance to side with them? That’s it! They knew I tried to stop the experiments and are thanking me. Well Aliens, I’m on your side now and I want to visit your world!”

You collect the guard’s guns and off you run through the hole in the wall. Your adventure begins….

Outline
You were a janitor at the Black Mesa facility. Your objective is to reach the portal that Gordon Freeman created, so that you can go to the Alien’s home world. Along the way you meet the security guards, army grunts and the deadly assiains. None of the original alien creatures attack you but there could be a few new ones who do.

With a bit more work I’m sure I could add a few extra details to make it more interesting, anybody want to contribute?

The Twist
After completing the mod the view shifts to a close-up of one eye of the character and slowly moves away from him. The view exits the key hole of a prison door. The character is seen staring at nothing while sitting inside a prison cell. You hear two guards talking:
Guard 1: “So what’s with him?”
Guard 2 “Dunno, he’s been like that for a few days now.”

Then there’s an explosion inside the cell and it starts all over again.

Is he mad? Was it all in his head? You decide.