The documentary film Abducted in Plain Sight features a sexual predator that spins a tale of alien abduction to control his twelve-year-old victim.
Alien Abduction is inspired by the actual phenomenon of the Brown Mountain Lights (a UFO phenomenon frequently reported in North Carolina), and recounts the ordeal of a family hunted down and abducted by aliens while on a camping trip.
Communion: It's about a man who has to come to terms with being abducted by aliens who probed him. It's treated like rape, and he even has to see a psychiatrist who specializes in rape victims.
Dark Skies: The Greys are experimenting on a typical suburban family and abduct one of its members.
Fire in the Sky: Loosely based on a true story, the movie doesn't focus on the abduction itself but on the struggle between those who are trying to prove it to be true and those who are trying to prove it to be false. Instead of believing the abduction, the police suspected Allan Dallas of murdering Travis Walton until Walton reappeared five days later.note It is worth noting that the abduction depicted in the movie is nothing like the account given by the real Travis Walton, whose story the movie is based on. In Walton's actual account, the aliens while frightening in appearance were not violent, and did not torture him.
In Flight of the Navigator, the protagonist wakes up 8 years after being abducted and returned to Earth, and hasn't aged at all because of time dilation caused by faster-than-light travel.
In The Fourth Kind, the protagonist is interviewing people who claim to have been abducted.
The reason beyond Bernard Phillips' apparent virgin birth in God Told Me To is eventually revealed to be aliens who abducted his mother and impregnated her through artificial insemination. And this is how the hero was made as well.
Guardians of the Galaxy begins with Peter Quill being abducted from Earth by the Ravagers. It turns out at the end of the film that they were hired by his father, but decided to keep him instead.
Honeymoon: Bea is mind-controlled, abducted and impregnated by beings that are implied to be aliens.
In Horse Girl, Sarah comes to believe that her missing memories and dreams about lying in a white room are evidence of her being abducted by aliens, who are using her as a "thermometer" to learn about Earth and leave her covered in bruises and scars.
In Independence Day, Russell Casse apparently was abducted by aliens, only nobody believed him and mocked him mercilessly about it (some even implying that his "alien abduction" was really some people who abducted him and abused him sexually) until they showed up. Of course, it's never entirely made clear if it was true, or if the aliens in the movie were even the ones who did it. If you accept the comics as canon, then it is, and they were.
Intruders: Most of the film deals with aliens abducting successive generations in the same families. At the end, aliens themselves reveal their reasons to the abductees.
It Came from Outer Space (1953). The aliens abduct humans both to copy their bodies (so they can covertly steal equipment to repair their spaceship) and as hostages. They have no malevolent intent, but believe their alien appearance will lead to conflict with the primitive humans.
In Mysterious Skin (which is also a book), Brian thinks this is what happened during a blank spot in his childhood. The truth is much, much worse.
Nope is centered around a California ranch dealing with a UFO abducting their horses. It then moves on to humans. Subverted as the film reveals the UFO is actually a singular Starfish Alien that is eating its victims rather than abducting them.
This is the premise of Predators, in which a bunch of killer humans (soldiers and criminals) are somehow abducted by the Predators and taken to a faraway planet to be hunted for sport.
The Signal: This is the true explanation for what happened to the trio of protagonists.
As you can guess from its name, the segment "Slumber Party Alien Abduction" from the anthology V/H/S/2 deals with a family hosting a slumber party when they come under an extremely chaotic attack by Greys. They all end up abducted, except the family dog who is both literally and figuratively kicked off their spaceship.
War God have the protagonist's sister getting abducted by Martians before returning to Earth a few weeks later on her own, delirious and nearly losing her mind, because the Martians have implanted their message inside her brain and is using her as herald announcing the upcoming Alien Invasion.
