In 2058, Earth will soon be uninhabitable due to the irreversible effects of pollution and ozone depletion. In an effort to save humanity, the United Global Space Force sends Professor John Robinson, his wife Maureen, daughters Judy and Penny, and young prodigy son Will on the spaceship Jupiter II to complete construction of a hypergate over the planet Alpha Prime, which will allow the population of Earth to be instantly transported and populate the new planet. Penny rebels by breaking curfew, while Will's prize-winning science experiment involving time travel goes largely unnoticed by John. Global Sedition, a mutant terrorist group, assassinates the Jupiter II's pilot, who is replaced by hotshot fighter pilot Major Don West, to his chagrin.
The family's physician Dr. Zachary Smith, a Sedition spy, sabotages the ship's on-board robot before launch, but is betrayed by his cohorts and left unconscious as the ship launches and the family enters cryosleep. The robot activates and begins to destroy the navigation and guidance systems, en route to destroying the family. Smith awakens the Robinsons and West, who manage to subdue the robot, but the ship is falling uncontrollably into the sun. Forced to use the experimental hyperdrive with an unplotted course, the ship is transported through hyperspace to a remote planet in an uncharted part of the universe.
Passing through a strange distortion in space, the crew finds two abandoned ships in orbit: the Earth ship Proteus, and another ship clearly not of human origin. They board the Proteus, with Will controlling the now-modified robot. They find navigational data to reach Alpha Prime, and a camouflaging creature Penny calls "Blarp", along with evidence suggesting the ship is from the future. They are attacked by spider-like creatures; one scratches Smith, and the robot's body is irreparably damaged but Will saves its computerized intelligence.
West destroys the vessel to eradicate the spiders, causing the ship to crash-land on the nearby planet, where another distortion appears. Will theorizes they are distortions in time, as his experiment predicted, but John ignores his input. Exploring the time bubble, he and West encounter a future version of Will and a robot he rebuilt with the saved intelligence. (The time-travel illusions in the 1967 Lost in Space television episode "Flight into the Future," such as a future statue of the Robot and descendants of Dr. Smith and Judy, are likely an influence on this part of the film.) The older Will explains that surviving spiders killed Maureen, Penny, and Judy. Constructing a time machine, the future Will intends to return to Earth to prevent Jupiter II from launching.
Young Will and Smith investigate the time bubble on their own. Smith tricks Will into handing over his weapon, but is foiled by a future version of himself, transformed by his spider injury into a spider-like creature, who has been protecting Will since the rest of the family was killed. The present Will and West return to the Jupiter II with an injured Smith and the robot in tow, while the future Smith reveals his true plan: He killed the Robinsons, but kept Will alive to build the time machine, so Smith could return to Earth and populate it with a race of spiders.
John, remembering that spiders eat their wounded, rips open Smith's egg sac with a trophy Will turned into a weapon. Smith’s spider army devours him and he is thrown into the time portal, ripping him apart. The planet’s increasing instability forces the Jupiter II to take off, but they are unable to reach escape velocity and are destroyed by the planet's debris. Realizing his father never actually abandoned them, and that he really does love him, Will sets the time machine to send John back to his family, but there is only enough power for one person. Saying goodbye to his family, the future Will is killed by falling debris, and John reunites with his living family.
Realizing they do not have enough power to escape the planet's gravitational pull, John suggests they drive the ship down through the planet, using the gravity well to slingshot them back into space. They are successful, but the planet turns into a black hole, and they activate the hyperdrive to escape. Using the Proteus’ navigational data to set a potential course for Alpha Prime, the ship blasts off into hyperspace.
William Hurt as Professor John Robinson
Mimi Rogers as Professor Maureen Robinson
Heather Graham as Dr. Judy Robinson
Lacey Chabert as Penny Robinson
Jack Johnson as Will Robinson
Jared Harris as Older Will Robinson
Matt LeBlanc as Major Don West
Gary Oldman as Dr. Zachary Smith / Spider Smith
Dick Tufeld as the voice of Robot
Lennie James as Jeb Walker
Mark Goddard as General
June Lockhart as Principal
Marta Kristen as Reporter #1
Angela Cartwright as Reporter #2
Edward Fox as Businessman
Gary A. Hecker as voice of Blawp
adapted from the 1965–1968 CBS television series of the same name (itself inspired by the 1812 novel The Swiss Family Robinson by Johann David Wyss).