The date is October 16, 1999, and it is zero minus one hour and fifteen minutes and holding. The Robinson family is taking their final pre-liftoff physical tests.
A panel slides open and a Colonel Smith emerges. He pulls the programming tapes from the environmental robot and installs a new program. The new program will instruct the robot to destroy vital stations on board the ship 8 hours after liftoff. A soldier finds the Colonel on board but Smith knocks him out, thn drops his body down a waste disposal shoot. Smith then contacts his superiors to report that his mission to sabotage the ship has been accomplished.
At zero minus thirty-three minutes the Robinsons are ready to board the ship. Smith is the Alpha Control Doctor. The General and Colonel Smith accompany the Robinsons as they board the ship. While on board Smith notices that the robot's power is turned off.
At zero minus three minutes, all the technicians are asked to disembark. The President is on television to send his prayers and wishes to the Robinsons. At zero minus two minutes, Smith replaces the robot's power pack and flips the power switch on. The Robinsons and Major Donald West enter the freezing tubes. The freezing tubes are activated at zero minus forty-five seconds. But all hatches become secured as Colonel Smith attempts to leave so Smith decides to strap himself in before liftoff and what would become certain death for him.
Smith rides out the liftoff but his extra weight has caused the automatic navigation system to miscalculate the ship's path through space and into a line of space rocks. Colonel Smith gets up just before the meteoroid storm hits the ship and quickly flips the power off on the robot but the switch gets stuck between on and off. As the saboteur goes to the ship's upper level, the robot activates and flips the switch to the on position. Smith attempts to contact Alpha Control without success and in a fit of anger smashes the communication panel. Fearing a certain disaster and sure death, Smith revives Major West so that he may pilot the ship to safety. In turn, West wakes the Robinsons. They learn that they are off course and must decide if they should continue to Alpha Centauri or try to return home. Smith demands to be taken back to Earth.
At takeoff plus seven hours and fifty-seven minutes, Smith notices that the robot's power is back on and rushes to the lower level to remove the robot's power pack. Major West turns off the artificial gravity to fix a problem just before Smith gets to turn off the robot's power. Smith pulls the power pack from the robot right at takeoff plus eight hours.
Will goes down to the lower level and talks to Smith. Smith fakes that he sees a virus growing on Will's tongue. He puts Will in quarantine and goes to the upper level to inform his parents. While Smith is upstairs, Will notices that the robot's power pack is missing and replaces it. The robot now carries out his program to destroy the ship's systems. Smith and West try to stop the robot and succeed but only after the ship goes into hyper drive, sending them far off course.
Tracking the out of control ship from Alpha Control, the President is contacted and told that the Jupiter 2 is hopelessly lost is space while John Robinson takes a space walk to fix the ship's NGS scanner. While outside the ship, his safety line breaks and Maureen suits up and shoots him a line using a rocket gun only it misses, leaving John drifting away into space.