In the near future, the solar system is being struck by mysterious power surges of unknown origin, threatening all human life. After surviving an incident on an immense space antenna caused by one of these surges, Major Roy McBride, son of famed pioneering astronaut H. Clifford McBride, is informed by U.S. Space Command (SpaceCom) that the source of the surges has been traced to the "Lima Project" base. The Lima Project had been set up to search for intelligent life from the farthest regions of the Solar System under Clifford's leadership, but nothing had been heard for sixteen years after they reached Neptune. A SpaceCom officer informs Roy that they believe Clifford may still be alive, and he is tasked with the mission of travelling to Mars to try and establish communication with him. Roy accepts the mission, and is joined by an old associate of his father, Colonel Pruitt.
After taking a commercial flight to the Moon, Roy and Colonel Pruitt are escorted by US military personnel to the SpaceCom lunar base. En route in lunar rovers, they are ambushed by scavenging pirates, who kill most of the group except for Roy and Pruitt. After reaching the base, a dying Pruitt is placed into intensive care.
Roy transfers to the Cepheus, a SpaceCom ship, on a flight to Mars. During the journey, the ship receives a distress signal from a Norwegian biomedical research space station. It seems abandoned, but an aggressive baboon (a research primate) test subject has escaped. It kills the ship's captain before being neutralized by Roy. Another baboon attacks, but Roy locks it in a module and ejects it, killing the baboon, and escapes the station with the captain's body. The crew of the Cepheus then ejects it out the airlock.
While landing on Mars, another power surge hits the Cepheus, forcing manual intervention. The interim captain finds himself too scared to fly, leaving Roy to take the controls and land the ship safely.
Having landed on Mars, Roy is taken to the underground SpaceCom base, where he briefly meets Helen Lantos, the facility Director, and is then tasked with recording voice messages to be sent to the Lima Project, in hopes that Clifford will respond. During one of the later voice recordings, Roy goes off-script with an emotional appeal to his father. Roy is abruptly taken off the mission, presuming a response has been heard and that his personal connection to the mission is deemed to pose a psychological risk to himself and the mission's success.
While being kept in a "comfort room", he is visited by Lantos, who reveals she was born on Mars and has only been once to Earth as a child. She also reveals that she is the daughter of Lima Project crew-members. She shows Roy classified footage from the Lima Project, revealing that Clifford's crew mutinied against him by trying to return to Earth, leading him to turn off their life-support systems, and that her parents were among the crew killed. She also tells him that the crew that brought him to Mars are soon heading to the Lima Project base themselves, where they intend to destroy it with a nuclear payload. The two decide that Roy is the only person who should confront Clifford, and Helen sneaks Roy out of the base, leading him to an underground lake beneath the rocket launch site.
As the rocket takes off, Roy climbs aboard. After he is discovered, the crew is instructed to neutralize him. Despite Roy's best efforts to keep the peace, the entire crew dies. During the long journey to Neptune, Roy, now alone, reflects on his relationship with his father, as well as that with his estranged wife, Eve. The isolation and stress of the mission take a toll on his mental condition, but after several weeks he arrives at the Lima Project.
While approaching the base in a small module, another surge strikes, damaging the module and forcing Roy to enter the base through a space-walk. Finding the Lima base nearly abandoned and its crew dead, he plants the nuclear payload then meets his father. Clifford, the sole survivor of the base, explains that the surges come from the ship's malfunctioning anti-matter power source, which was damaged during a mutiny. Clifford reveals that he continued to work on the project all these years, refusing to lose faith in the possibility of non-human intelligent life.
Despite his father's protest Roy arms the payload and prepares to return to his ship with Clifford, who uses the thrusters on his spacesuit to launch himself into deep space, refusing to go back to Earth. Roy tries to save him, but Clifford refuses the help, leaving a distraught Roy to watch his father drift away in Neptune's orbit. Alone, Roy manages to thrust himself back onto his ship, going through Neptune's rocky ring using a piece of the Lima Project ship's hull to shield himself, while also bringing along with him the data retrieved from the base. Without enough fuel to return on his own power, he uses the shock-wave from the explosion to propel the ship home.
Finding that the Lima Project data strongly suggests that humans are the only intelligent life in the universe after all, Roy finds himself imbued with a renewed desire to reconnect with those closest to him, and returns to Earth with a new-found sense of optimism. Expressing his opinions in a psychological evaluation, he then reconnects with his wife.
- Brad Pitt as Roy McBride
- Tommy Lee Jones as Clifford McBride
- Ruth Negga
- Jamie Kennedy as Peter Bello
- Donald Sutherland