The most intriguing movies leave you with a question that only you can answer. In the film Contact, the viewer is left with the question of whether Jodie Foster talked with an alien who contrived to look like her father or if the whole thing was an elaborate hoax played by a dying old man.
One of the odder phenomena in science fiction is the alien bug eyed monster who is so alien to us that it has acid for blood and impenetrable skin and somehow it still wants to get into our bodies-Aliens for example. Although this premise makes for great and thrilling movies it is more than a little illogical. It's kind of like expecting the average, normal human being to be interested in slugs and slime molds. For biological reasons we are usually most interested in a range of textures that are similar to our own. If we weren't, mating and reproduction would never take place. Nature does have cases wherein males and females look very different but more often than not, size is and/or colors are the only real differences. Spiders dig spiders and ducks go for ducks. Spiders don't go for ducks-not even as food.
The Hitchiker's guide to the Galaxy, although a very silly book and movie, did have one thing right. If a species was truly alien to us, it would pay no more attention to us than we would to ants at a picnic. There was a famous science fiction story called Roadside Picnic that was based on just this premise. The most alien creatures I can think of on planet earth live near volcanic vents in the deep ocean. The water is boiling hot and probably acidic. It would kill us to be exposed to it for even a few seconds yet at least thousands and maybe billions of creatures thrive there. This reminds us of two things. If the aliens are sufficiently different, we may not perceive them at all or if we do perceive them, it may not seem to us that they are not alive.
One of the more stunning things about the creatures that live in a hot acid bath under the sea is that they have DNA just as we do. This brings up the point that we are not ready to encounter true aliens whose chemistry and biology are radically different from out own. As the movie War of the Worlds and the science fiction story Roadside Picnic assert, we may not want to come to the notice of a truly alien species. What do you do when the ants get into the food at a picnic?
In a series and movie like X-Files they do bring up the notion that aliens might want to change us and the planet to forms more suitable for them. This seems likely for the truly alien species. After all, we have a lot of water here and although an alien aquatic species might find that water very appealing, they would have absolutely no use whatsoever for any land based creatures.
I rather like the 12 Monkeys premise in a movie. It has some of the best elements of a good science fiction story. At different points of the story the viewer is forced to decide what is real and what is not. Who is telling the truth and why. And finally we are forced to the conclusion that we did some horrible thing to ourselves. We are the aliens.
The Movie Millennium shared several thematic traits with 12 Monkeys, such as the use of time travel and the notion that we did the future catastrophe to ourselves. The fact is that if something that seems far out, futuristic, and yet it looks like us-humanoid with bilateral symmetry-shares our DNA, and seems fascinated to an extraordinary degree with us, then it's us. Not methane breathing silicon squids from Uranus. Time travel is theoretically possible and humans are not wise and selfless enough to leave our own history alone. As was depicted in the movie The Sound of Thunder, we are more than likely to wipe out our own history by futzing around in our past trying to "fix" things.
An intriguing offshoot of the "We're the Aliens" genre is the notion that we are stuck in a simulation. Matrix is the most popular exemplar in this group. Unlike Matrix, in the real world, if the programmer did find out we were screwing up his program, he would simply stop the simulation. There are a number of scientists who have given the notion of simulated existence a great deal of thought. They have come to the conclusion that over the course of human history there will be a great many more simulations of reality than actual reality. Such an analysis leads to the inevitable conclusion that any given individual is more likely to be simulation than a real, independent entity. Fortunately, no one takes this seriously. The moral and ethical consequences would be horrendous. All the bit players in Matrix movies are massacred by the ones who think the whole thing is a simulation.