This is a really imaginative idea. I think that you could definitely create a longer story--or even a novel--with what you have here.

The dialogue is very strong in some places, and weaker in others. You have a lot of explanation of the "history" to go through, which is why I think this would work even better as a longer story, because you could spread it out a little more. Also, there were a lot of lines that don't have a "he said" or "she said" after them, which have the potential to confuse a reader. Maybe you could break them up with some description. For example:

"Everyone makes mistakes. You somewhat made up for yours by saving me”

“’Saving’ one person doesn’t make up for a whole world of people”

Can turn into:

Everyone makes mistakes," Fiona said matter-of-factly. "You somewhat made up for yours by saving me.” She hadn't thought of it that way before now. He really -had- saved her. If it hadn't been for him, she would have been dead by now. It didn't really matter, though--it was either dead then or dead a little later. The concept of a long lifespan had faded long ago.

“’Saving’ one person doesn’t make up for a whole world of people,” Nate contested, pulling on his cigarette.

Or whatever, but you get the idea. People move and think while they're talking, and it helps them show who they are. Do you ever read your dialogue aloud? I know, I'm always afraid I'll sound like a crazy person if someone catches me, but if you don't, you should try it. People take a lot of natural pauses, and usually can't get all of the words they want out.

It's great that you have such an enormous idea, and the ending is creative. With the ending, don't feel the need to emphasize and reemphasize the fact that they're not sure if it's an enemy or a rescue team. A smart reader will pick up on this uncertainty with one mention.

Good luck! You've got a great start.

-K.