I have considered a story where at the end it turns out that the only member of the surviving characters who is human is the one everyone assumed was not. It would be a sort of standard, "Aliens take over human's bodies," plots at first glance, but on closer inspection would have a number of differences.
I actually don't remember a lot of what I was originally thinking about it, but I do remember that the above was based on two key points. The first was that the aliens couldn't tell who else was an alien, which meant that they, as much as any human, were left guessing who was and who wasn't. The other was that the surviving human was the only one of a group of mixed aliens and humans willing to say, "I don't care that we very definitely know that this person is an alien, I don't care that there might be an invasion on the way or a ticking timebomb or whatever, I don't care if we might learn valuable information that could save lives, I'm not going to stand by and let you torture someone." Which promptly got human branded an alien and thrown in captivity. (Later to be broken out by a group of aliens, none of whom admitted to being aliens or knew their collaborators were aliens, who thought human was right about that but sure as hell weren't going to say it publicly.)
Human basically spent the rest of the story trying to do two things:
1 Not die.
2 Keep the much abused definitely-alien alien safe.
Thing two basically convinced everyone that human was an alien. "We're fleeing an apparent alien invasion and you're trying to protect an alien? This makes sense how?"
I don't remember a lot of details beyond that. Eventually the entire small town would be destroyed when someone decided that taking off and nuking the site from orbit was the only way to be sure. The aliens in the group of survivors weren't looking for world domination but instead to escape from witch-hunt-central.
Trying to fill in the blanks I think I'd do it something like this:
For most aliens they're still basically the same as they were when they were human, they might think somewhat differently and perceive somewhat differently, and have different abilities, but really the biggest change when they stopped being human was the knowledge that they weren't human anymore. There were a variety of different reactions and while there might have been a certain amount of cackling, "I shall take over the world," or some, "I'm not human so I don't have to follow petty human ideals of right and wrong," most of the negative reaction was borne of fear. (Oh my god, if people find out I'm an alien they'll hunt me down and kill me, I have to get them before they get me!) So you sort of get them justifying a preemptive war on humanity as a means of self defense, which isn't helped by the human reaction when they realize, "Hey, something is wrong here," which as previously mentioned includes witch-hunting and torture.
The town basically goes to war with itself.
One of the reasons that the formerly human aliens don't have any unified direction is that they really weren't created on purpose. Alien ship crash landed, and the dying, lets say queen, went into involuntary spawning mode as a result of her injuries. The resulting creations were largely blank, and thus when they combined with humans didn't bring all that much to the table psychologically. Then the queen happened to notice that ship had managed to injure a human, and while alone either of them would die, together they'd live, and that's where definitely-alien alien comes from.
And I think I saw them escaping the town using a series of tunnels, perhaps a used up mine.
It finally comes out that almost every member of the party is an alien when the subject of what to do with definitely-alien alien comes up now that they've escaped almost certain death. Everyone gets nervous, and it is revealed that actually, the all agree. None of them want to do anything, human on general principles, aliens because they're finally in a position where they think they might not be put in danger by saying, "Aliens aren't all bad, I know because I am one." (They're all positioned such that they could probably run away.)