The Recall

Aliens come to Earth, beam some humans onto their spaceships, and go down to the surface looking for other people. A group of teenagers run from the aliens, and meet a former astronaut who was abducted and experimented upon by the aliens years ago. He explains that the aliens have visited Earth several times in the distant past, and have guided the evolution of life on Earth. He's been preparing for their return, and he ambushes some of the aliens. The children all end up being taken to the spaceship where they are among a few thousand humans who are abducted, then returned to Earth. The government declares that it's going to put the abductees in quarantine when they return, but it ends up trying to kill them. However, the teenagers survive the government attack due to the superpowers they were given by the aliens.