I wrote the following story for a couple of mod developers who were looking for a specific co-op storyline. The idea of writing a draft story specifically for a Co-Op mod is an interesting one and to my knowledge that has never been done, nor has a mod been made specifically for two players. However, there is a new game called Army of Two that seems to be exactly that!
It’s probably not hard to create situations that require two or more players to win but it is a bit harder to include that into a story outline. I think I have a realistic setting that also would allow for more in-depth story telling if required.

The two main characters are called Peter and Steve Johnson. They are brothers and best friends. They have been in the resistance since the moment it was formed, just after the Combine conquest.
As well as playing their part in the rebel attacks; they are also on a personal mission. Unbeknown to their rebel colleagues, Peter and Steve have a younger brother. His name is Michael and he has not been heard from since the Combine arrived. He was away university at the time of the invasion.
Secretly Peter and Steve have been looking for information about him. They believe the Combine probably captured him and goodness knows what has happened to him?

During a recent mission they are certain that they saw Michael being forced onto a transport train bound for a Combine Conversion centre. However, it is unclear whether this was his destination or one of the stopping points along the way.
Without hesitation the brothers agree that they must rescue him. Unable to breakaway from the attack, they decide to leave at night; to not only avoid the Combine patrols but also the rebel guards. If spotted they will be stopped because they know too much about the rebel organisation and objectives to be captured by the Combine. They may also be shot for deserting!
They eventually reach the train yard and hide aboard a train. At every stop they get off and search for their brother or information about him. Finally at the end of the line they reach a Combine Conversion Centre. This is where humans are converted into Combine workers. It is also a Combine training facility, with many different buildings and sections: shooting ranges, burnt-out building to practice entering and clearing etc.
After killing as many Combine soldiers as possible they finally find Michael. Here the story can take a twist or have the normal “And they all lived happily ever after “ ending!

THE HAPPY ENDING: They simply need to protect Michael because he has no weapons and escape into the countryside and live freely.
THE TWISTED ENDING: They are too late and Michael has been converted into a Combine soldier. They have to make a choice about whether to kill him or let him live. If they choose to kill him then this is like a boss level.
My choice is the twist because I think it is good to confront difficult choices in games. This adds a level of realism often missing. Nobody wants to kill his or her brother, but they also have to consider what is better for him – a quick death or a life of servitude under oppressive rulers with NO chance of recovery!

I wrote the story specifically for an episodic series. Each train stop is another type of location with perhaps a little more information given about their brother and where he is being taken. I haven’t thought about the deeper elements because the story was rejected. I feel the storyline is both realistic and interesting. It would allow the level designers plenty of scope regarding themes or locations.
I personally envisage the Combine Conversion Centre to be at the end of the line, both geographically and metaphorically. Somewhere on the coast, giving the feeling that there is nowhere left to look and surrounded by forest which gives the feeling of being caged in.
The centre itself can consist of a few distinct sections: Underground processing area, small derelict town used for training drills, a training course within the forest, in fact there could be many different areas.
One advantage of this idea is that there would be very little, if any, new textures or models needed. This could be built with all the assets within HL2.
If anybody or team is interested in developing this idea I will be more than happy to supply additional ideas for the stopover points, along with more details about the brothers and the Combine’s reason for capturing Michael.