In Mexico’s Sonoran Desert, French scientist Claude Lacombe, and his American interpreter David Laughlin, along with other government scientific researchers, have discovered Flight 19, a squadron of World War II airplanes that disappeared more than 30 years earlier in the Bermuda Triangle. The planes are all intact and operational, but there is no sign of the pilots. An old man who was there last night claimed that “the sun came out at night, and sang to him”. Meanwhile, at an air traffic control center in Indianapolis, controllers listen as two commercial airline flights are nearly hit by an unidentified flying object (UFO). In Muncie, Indiana, 3-year-old Barry Guiler is awakened in the night when his toys turn on all by themselves. Fascinated, he gets out of his bed and goes downstairs, and discovers someone or something (off-screen) in the kitchen. Playfully, he runs away from the house, forcing his mother, Jillian, to chase after him.
Investigating one out of a series of sudden and large-scale power outages across Indiana that same night, electrical maintenance worker Roy Neary experiences a close encounter with a UFO when it hovers over his truck, affecting all of the truck’s electrical systems and lightly burning the side of his face with a bright light. Chasing after it, he almost hits Barry and Jillian, and they encounter smaller UFOs hovering low to the ground as they fly down the road, as if they were cars. Neary follows police cars that are pursuing them, but the objects fly off into the night sky. Roy subsequently becomes greatly fascinated by UFOs, much to the dismay of his wife, Ronnie. He also becomes inexplicably, yet increasingly obsessed with making models of a mountain-like shape. Jillian also becomes obsessed with sketching a unique-looking mountain.
Lacombe, Laughlin, and various United Nations experts continue investigating increasing UFO activity and strange, related occurrences across the globe, such as finding the SS Cotopaxi—a ship that also disappeared in the Triangle 50 years earlier—inexplicably in the Gobi Desert. Witnesses in Dharamshala, India report the UFOs emit a particular sequence of five musical tones: D’, E’, C’, C, G. Scientists broadcast the sequence to outer space and receive, in response, a seemingly meaningless string of six numbers repeated over and over (as short radio pulse sets). Using his background in cartography, Laughlin recognizes the numbers to be a set of geographical coordinates that are pointing to Devils Tower, Wyoming. Lacombe and the U.S. military converge on Wyoming and Devil’s Tower. The Army evacuates the entire area around Devils Tower by planting false reports in the media that a train wreck has spilled a toxic nerve gas, all the while preparing a secret landing zone for the UFOs and their occupants.
Meanwhile, Jillian is terrorized in her home by a UFO which descends from clouds it appears to take with it, and causes appliances in her house to activate (including a telephone it has ring starting to play the five musical tones when Jillian answers, faster and faster until the scene ends) as unseen beings try entering the house in every possible way, initially stopped by Jillian, until Barry, who joyfully seems to want to help the beings do it, is abducted by them. Shortly after, Roy’s increasingly erratic behavior causes Ronnie to leave him, taking their three children with her. When a despairing Roy inadvertently sees a television news program about the train wreck near Devils Tower, he recognizes that the butte is what the mountain in his models is. Jillian also sees the same broadcast, and she and Roy, as well as others with similar visions and experiences, travel to the site in spite of the warnings about nerve gas.
While most of the civilians who are drawn to the site are apprehended by the Army, Roy and Jillian persist and make it to the Army’s secret landing zone just as dozens of UFOs appear in the night sky. Scientific specialists at the site begin to try to communicate with the UFOs by the use of light and sound from a large electrical billboard that is being controlled by a synthesizer. After the UFOs leave, an enormous mothership lands at the site, also using light and sound to teach the specialists the aliens’ basic tonal vocabulary. It then releases the missing pilots from Flight 19, as well as the missing sailors from the Cotopaxi and many other long-missing people, all from different past eras and all of whom have not aged since their abductions. Barry is also returned and reunited with a relieved Jillian.
As the aliens finally emerge from the mothership, the government officials, convinced by Lacombe, decide to include Roy in a group of people whom they selected as potential travellers to join the mothership, and hastily prepare him. The aliens select Roy to join them on their travels, and after Roy enters the mothership, one of the aliens pauses for a few moments with the humans. Lacombe uses Curwen hand signs that correspond to the five-note alien tonal phrase. The alien replies with the same gestures, smiles, and returns to the ship which ascends into space.