I just finished Bangkok Dangerous and would so love to do something like that, well only the character xD
What I had in mind was that my character would be a ninja(xD hitman if you prefer) and he fell hard once. He tried to keep their relationship secret, however, he comes home one day to find her dead. He's out for revenge while taking other jobs to keep his enemy in the dark as to were he is actually located.
Now your character can either witness him killing his next target or they can be his next target. Either way he has to take them with him to make sure his identity isn't revealed. He continues his quest and just drags your character along with him. He is cold and cruel in ways, however, he loves children. He will refuse to even pull a gun if a child is in the room. His targets figure it out, but none live to tell about it.
I figure as they travel they slowly develop feelings for each other. Yours figures it out quicker than mine. I kind of have an ending for it but >.< I don't want to put it here to ruin for any who read and I don't know if you would want that ending.
This can be Yaoi or hetero. It can be Yuri, don't let my pronoun discourage you