Nearing the end of a long mission exploring deep space, the spacecraft USS Palomino is returning to Earth. The crew consists of Captain Dan Holland, First Officer Lieutenant Charlie Pizer, journalist Harry Booth, ESP-sensitive scientist Dr. Kate McCrae, the expedition's civilian leader Dr. Alex Durant and the robot V.I.N.CENT ("Vital Information Necessary CENTralized").
The Palomino crew discover a black hole in space with a spaceship nearby, somehow defying the hole's massive gravitational pull. The ship is identified as the long-lost USS Cygnus, the ship McCrae's father served aboard when it went missing. Deciding to investigate, the Palomino encounters a mysterious null gravity field surrounding the Cygnus. The Palomino becomes damaged when it drifts away from the Cygnus and into the black hole's intense gravity field, but the ship manages to move back to the Cygnus and finds itself able to dock to what initially appears to be an abandoned vessel.
The Palomino crew warily boards the Cygnus and soon encounter the ship's commander, Dr. Hans Reinhardt, a brilliant scientist. Aided by a crew of faceless, black-robed android drones and his sinister-looking robot Maximilian, Reinhardt explains that he has lived all alone on the Cygnus for years. After the ship encountered a meteor field and was disabled, he ordered the human crew to return to Earth, but Kate's father chose to remain aboard and has since died. Reinhardt then reveals that he has spent the past 20 years studying the black hole and intends to fly the Cygnus through it. Only Durant believes it is possible and asks to accompany Reinhardt on the trip.
The rest of the Palomino crew grow suspicious of the faceless drones' human-like behaviour: Booth sees a robot limping and Holland witnesses a robot funeral and discovers the Cygnus crew's personal items in the ship's living quarters. Old B.O.B. (BiO-sanitation Battalion), a battered early model robot similar to V.I.N.CENT, explains that the faceless drones are in fact the human crew, who mutinied when Reinhardt refused to return to Earth and had been lobotomized and "reprogrammed" by Reinhardt to serve him. McCrae's father had led the mutiny and was killed. Using telepathy, V.I.N.CENT tells Kate the truth about what happened. When Kate tells Durant, he removes the reflective faceplate from a "drone" to reveal the face of a crew member. Durant tries to flee the bridge with Kate, but Maximilian kills him, contrary to Reinhardt's wishes. Reinhardt takes Kate prisoner, ordering her to be taken to the hospital to be lobotomized by his security robots.
As the process begins, Holland rescues Kate, along with V.I.N.CENT and B.O.B. Meanwhile, fearing the situation is escalating dangerously, Booth attempts to escape alone in the Palomino. Reinhardt orders the craft shot down, but the weapons fire sends the ship crashing into the Cygnus, destroying its port-side anti-gravity forcefield generator. A meteor storm then destroys the starboard generator. Without its null-gravity bubble, the Cygnus starts to break apart under the black hole's huge gravitational forces.
Reinhardt and the Palomino survivors separately plan their escape aboard a small probe ship used to study the black hole. Maximilian goes to prepare the probe shortly before Reinhardt is pinned by falling debris. His lobotomized crew stand motionless as he struggles. Maximilian confronts the others and fatally cripples B.O.B. moments before he himself is crippled by V.I.N.CENT and drifts out into space. Holland, Pizer, McCrae and V.I.N.CENT reach the probe ship, only to discover the controls locked onto a flightpath through the black hole. It then plunges across the hole's event horizon.
In a surreal sequence inside the black hole which resembles Heaven and Hell, it appears that Reinhardt becomes merged with Maximilian, and they are seen standing on a high rock overlooking a burning, hellish landscape populated by dark robed figures resembling the Cygnus drones. Next, a floating, angel-like figure with flowing long hair passes through a cathedral-like arched crystal tunnel. The probe ship then emerges from a white hole and is last seen flying through space towards a planet near a bright star.