I have an idea for one with a twist.
All the players are crew aboard a starship returning to Earth. Several crew have been infected by aliens and must eat the crew to stay alive.
So far, so Werewolf.
Some members of the crew have vital roles on the ship and killing them (either being eaten or lynched) may doom the ship before they reach Earth, killing everyone aboard.
The aim of the aliens is to have at least one survivor by the time they reach Earth. The aim of the crew is to kill the aliens before they land on Earth.
Both the crew and the aliens lose if too many essential personnel are killed before they reach Earth.
The aliens will have the equivalent of a psychic, so we might get an interesting situation where aliens have to work together to stop the crew from lynching a non-alien.
That sounds really cool, but I imagine all that would happen is people would just tell everyone they are an essential personnel. I mean, why wouldn't they? There would be no downside because nobody would want to kill you and you would be essentially immune.
I think there could be a way to fix this though. There could be a suicidal nut job. The goal if you are him is to make sure both teams lose. He could be able to kill people, but he has a limited amount of turns he can kill people. So if there are 5 essential crew members, he only has 6 turns he can kill somebody.
A la 'Sunshine?' I like it.
What if we reverse it.
Say a western town is seeing a lot of UFOs. The aliens have replaced a few of the humans. The goal of the aliens is to abduct all the humans. However they don't have the man power to abduct everyone at once and can only get one person a night.
Now instead of a Ninja we have a "hero". This person is immune to the alien's brainwashing technology. As such if they are abducted, they will escape and learn the identity of all the other aliens.
Now, aliens CAN choose to "abduct" one of their own. Obviously this won't help them get the needed humans and puts them behind by a turn, but it does allow them to claim that the abducted alien is the Hero and finger others. Of course they'll be proven wrong very quickly after one of the lynches, but it does allow a directed lynch and an "abduction" at night.