In 2020, the Mars I mission launches for planet Mars, commanded by Luke Graham (Don Cheadle). Upon arrival, the team discovers a bright white formation in the Cydonia region, which they suspect is an extrusion from a subsurface geothermal column of water, useful to future human colonization. After reporting this to the Earth-orbiting World Space Station, they go to investigate the formation and hear a low sound on their communications system. Radar initially reports that the formation is metal, but when they increase power to the radar, a large vortex appears and kills everyone except Luke. After the vortex subsides, the formation is revealed to be part of a large humanoid face.
The event creates an electromagnetic pulse the space station observes, after which it receives a distress message from Luke. Realizing Luke couldn’t have left because the pulse would have damaged the computer system of the ERV (“Earth Return Vehicle”), they repurpose the Mars II mission into a rescue.
Months later, as Mars Rescue, consisting of Commander Woody Blake (Tim Robbins), his wife Terri Fisher (Connie Nielsen), recent widower Jim McConnell (Gary Sinise), and technician Phil Ohlmyer (Jerry O’Connell), nears Mars orbit, they discover that all satellite imagery of the formation area is covered with static. Micrometeoroids breach the ship, causing damage that leads to the engines blowing up. The crew are forced to abandon ship and take refuge in the REMO (“Resupply Module”) orbiting Mars. Woody launches himself at the module and manages to attach a tether to it, but is knocked off into space. Terri tries to rescue Woody, but knowing she would run out of fuel before reaching him, Woody removes his helmet, killing himself to save her.
The survivors arrive on the surface of Mars, and begin repairing the ERV. They find Luke living in a greenhouse, who shows them pictures of the face, and reveals that the pulses in the low sound they heard represented a 3D model of human-like DNA, but missing a pair of chromosomes. Jim determines they must complete the sequence to pass a test, and they send a rover to broadcast the completed signal via radar. Following the transmission, an opening appears in the side of the structure. With a massive dust storm approaching Jim, Terri, and Luke head to the formation, while Phil stays to finish repairing the ERV. Phil is ordered to launch, with or without them, before the storm hits.
The three astronauts enter the opening, which seals behind them. A three-dimensional projection of the solar system depicts the planet Mars, covered with water, being struck by a large asteroid and rendered uninhabitable. A projected humanoid alien reveals that the natives of Mars evacuated the planet in spaceships, one in which was sent to seed Earth with DNA in the hopes that it would create lifeforms who could one day land on Mars and be recognized as descendants. An invitation is offered for one of their group to follow the Martians to their new home. Jim accepts the invitation, bidding farewell to Terri and Luke, and is sealed inside a small capsule. Terri and Luke race back to the ERV and arrive just as Phil is about to take off. They barely escape the dust storm into space as Jim’s capsule is launched from the crumbling formation and past them toward the Martians’ home.