Dr. Eleanor "Ellie" Arroway (Jodie Foster) is a gifted scientist, encouraged as a child by her father (David Morse), who has long since passed away. She presently is working for the Search for Extra-Terrestrial Intelligence (SETI) program at the Arecibo Observatory in Puerto Rico. She and her colleagues listen to radio transmissions in hopes of finding signals sent by extraterrestrial life. Government scientist David Drumlin (Tom Skerritt) pulls the funding from SETI as he believes it's a futile exercise. After 13 months of soliciting funds in vain, Ellie gains funding from billionaire industrialist S. R. Hadden (John Hurt), who has been following Arroway's career and allows her to continue her studies at the Very Large Array (VLA) in Socorro County, New Mexico.
Four years later, with Drumlin pressuring to close SETI, Arroway finds a strong signal repeating a sequence of prime numbers, apparently emitting from the vicinity of the star Vega. This announcement causes both Drumlin and the National Security Council, led by National Security Advisor Michael Kitz (James Woods), to attempt to take control of the facility. As Arroway, Drumlin, and Kitz argue, the team at the VLA discover a video source buried in the signal: Adolf Hitler's welcoming address at the 1936 Summer Olympics in Berlin. Arroway and her team postulate that this would have been the first significantly strong television signal to leave Earth's atmosphere, which was then transmitted back from Vega, 26 light years away.
The project is put under tight security and its progress followed fervently worldwide. President Bill Clinton and Drumlin give a television address to downplay the impact of the Hitler image, while Arroway learns that a third set of data was found in the signal; over 60,000 "pages" of what appear to be technical drawings. Government specialists unsuccessfully attempt to decode the drawings, later decoded by Hadden. He explains that the pages are meant to be interpreted in three dimensions, which reveals a complex machine allowing for one human occupant inside a pod to be dropped into three rapidly spinning rings.
The nations of the world come together to fund the construction of the machine at Cape Canaveral on top of Launch Complex 39. An international panel is put together to select a candidate (including both Arroway and Drumlin) to travel in The Machine. While Ellie is one of the top selections, her lack of religious faith is noted by Palmer Joss (Matthew McConaughey), a trusted friend and one of the panel members. Drumlin is ultimately selected. On the day of testing the machine, a religious fanatic (Jake Busey) obliterates the machine completely in a suicide bombing, killing Drumlin and everyone else onboard.
However, after the destruction, the mysterious and secretive Hadden reveals to Arroway that there is in fact a second machine, hidden in Hokkaido, Japan, and in fact Arroway will be the "pilot."
Arroway begins her journey, outfitted with several recording devices. When the pod travels through a series of wormholes, she is separated briefly and can observe the outside environment. This includes a radio array-like structure at Vega, and signs of a highly-advanced civilization on an unknown planet. She finds herself in a surreal landscape similar to a picture she drew as a child of Pensacola, Florida, and is approached by a blurry figure that resolves into that of her deceased father. Arroway recognizes him as an alien taking her father's form, and attempts to ask questions about extraterrestrial life. The alien deflects her questions, explaining that this journey was just humanity's "first step" to joining other space-faring species.
Arroway considers these answers and falls unconscious, finding herself on the floor of the pod where she is being repeatedly called by the machine's control team. She learns that from all external vantage points, she and the pod merely dropped through the machine. She insists that she was gone for approximately 18 hours, but her recording devices only show static. Kitz resigns as National Security Advisor to lead a congressional committee to determine if the machine was an elaborate hoax designed by Hadden, who has since died. Arroway is described as an unwitting accomplice in a hoax orchestrated by Hadden; she asks them to accept her testimony on faith. Kitz and White House Chief of Staff Rachel Constantine (Angela Bassett) together reflect on the fact that Arroway's recording devices contained static, but contained 18 hours of it. Arroway is given continued grant money for the SETI program at the Very Large Array.