I like the idea that our duo gets assigned a mission, although I think it should be large enough that there would be more than one team going. That way, we can play around with their relationship in front of other people, as well as away from them.

... How about this. For some reason or another, our guys leave halfway through this mission, and when they return to the Organization they learn that the teams who remained were all butchered, and suspicion has fallen on... one of them. Not both. They have to figure out who did it while under constant scrutiny. This antagonistic force is looking to break down/ take over the organization, and turn it into the evil organization that we were considering before. The best way to do that is break it from the inside, and, for some reason... our characters are an ideal place to start.

That could get a nice mix of conspiracy, action, and conflict, mixed in with the daily life of the Organization members, and the brunt they have to take from a public that hates them. Because I do believe that the Organization has to get its hands dirty fairly often. And some, maybe even most, people don't support it. But it isn't necessarily cruel or bloodthirsty.

Of course, all the while, the humans are, for one reason or another, drawing closer to figuring out about the existence of the Walkers. Perhaps a halfbreed child between a human and one of the races? Or another malignant force that wants the humans to wipe out the Walkers?

Any of that sound good to you?