In A.D. 2045, the Planet Earth is in ecologic crisis as a consequence of pollution and overpopulation. Meanwhile, automated interplanetary missions have seeded Planet Mars with atmosphere-producing algae as the first stage in terraforming the planet. Twelve years later, when the oxygen quantity produced by the algae is inexplicably reduced, the crew of Mars-1 must learn why, and continue the mission of terraforming the red planet for human colonization.

En route to Mars, the crew get to know one another through discussions about science, spirituality, and religion. Quinn Burchenal, the geneticist (Tom Sizemore), is an agnostic. Aging scientist and surgeon Bud Chantillas (Terence Stamp) is philosophical, having come to believe long ago that "science could not answer any of the really interesting questions." Mechanical systems engineer and "space janitor" Robby Gallagher (Val Kilmer) acts as Chantillas's protégé, and flirts with the spaceship's beautiful, but no-nonsense commander, Kate Bowman (Carrie-Anne Moss). Also on board is arrogant pilot Ted Santen (Benjamin Bratt) and Pettengil (Simon Baker).

Soon the ship arrives to Mars orbit, but a solar flare disrupts key systems, complicates their orbit and forces Bowman (Moss) to remain aboard and repair them, while the others land. Their first goal is to locate an automated habitat established earlier on Mars to manufacture food and oxygen in preparation for the crew's arrival.

The landing craft is damaged entering the Martian atmosphere, veers off course, and crash-lands far from their landing zone near the habitat. In the process, they lose track of "AMEE", a military robot that is their "Mars surface navigator." Moreover, Chantillas was critically injured in the crash landing, and they have insufficient air to take him to the habitat where his ruptured spleen could be attended. With limited air, Chantillas tells them to leave him behind and complete the mission.
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