(Character A) woke up alone in a ditch in a small town in the middle of Nebraska. He had 500 dollars in his pocket, a set of skills no one should possess, and no name, friends or family. He spent 3 years making a life for himself, and no one ever came to claim him. By this time he has a steady girlfriend, is holding down a job as a bartender, and has given up on ever finding out just where he came from. Little does he know...he is a spy. Yep. Top-secret James Bond crap. Think Bourne Identity but the government actually thinks he is dead. He doesn't get it, and he would never have gotten it until (Character B) rolled in to town. (Character B) just couldn't give up on him. His old partner, (Character B) has been with (Character A) through thick and thin and no way would he give up the search to find the person he knew in his heart wasn't dead. Maybe because he had a tip-off - or maybe just because (Character A) was way more to him than just a partner.
Government could be stalking them, other people could, it could be taken in a lot of different directions, I hope! I'd be taking Character A and would probably use a Chris Pine, Gaspard Ulliel, or Clive Owen for dudes or an Angelina Jolie, Megan Fox, Olivia Wilde or Bryce Dallas Howard, but I'm flexible.
Alternatively, I'd be really down for a Kirk/Spock or Kirk/McCoy line. That is all!