In 2058, Earth faces imminent destruction due to severe pollution, leading the United Global Space Force, the governing body of the planet, to embark on a desperate mission. Professor John Robinson (William Hurt), the lead scientist of the Jupiter Mission, is tasked with guiding his family—his wife Maureen Robinson (Mimi Rogers), their daughters Dr. Judy Robinson (Heather Graham) and Penny (Lacey Chabert), and their son Will (Jack Johnson)—to the habitable planet Alpha Prime. Their objective is to construct a hypergate in orbit, a vital component for colonization and the eventual evacuation of Earth's inhabitants.
The Jupiter 2, with its advanced hyperdrive allowing for faster-than-light travel, is central to their plans. However, the urgency of their task escalates when members of the Global Sedition terrorist group launch an attack on the hypergate under construction, resulting in the death of the spacecraft's pilot, Captain Daniels. Entering the fray is Major Don West (Matt LeBlanc), a skilled fighter pilot from the hypergate defense force. In a daring maneuver, he neutralizes the enemy threats but faces scrutiny for prioritizing a fellow pilot's life over protocol. Seeing great potential in West, Professor Robinson selects him as the new pilot for the Jupiter 2 despite Major West's initial reluctance.
Complicating matters is Dr. Zachary Smith (Gary Oldman), the medical officer of the mission, who is coerced by the Global Sedition to undermine their efforts. He betrays his team by reprogramming the ship's robot to sabotage their voyage. Left as an unwitting stowaway, Smith’s actions lead to the spacecraft veering dangerously close to the Sun. Realizing their dire situation, Major West and Professor Robinson devise a plan to fly through the Sun’s intense heat, intending to utilize the ship's hyperdrive.
Unexpectedly, their ship becomes disoriented, landing them in an unfamiliar locale within the galaxy. Here, they encounter a phenomenon they dub a "hole in space"—which they speculate might be a gateway to the future. Shortly after, they come across the Proteus, a ship from the future. It is implied that one of its older crew members is a friend of Major West; however, the vessel is perilously infested with deadly silicon-based lifeforms. In their escape, they lose control of their robot and Major West makes the controversial decision to destroy the Proteus to eliminate the threat, resulting in damage to the Jupiter 2.
As tensions rise, Professor Robinson and Major West clash over their dire circumstances, but Maureen intervenes with a proposal to refuel the damaged ship using a mysterious energy source located within a hazardous bubble. Meanwhile, they face shocking revelations about time distortions and alternate versions of themselves on this ominous planet, including a corrupted Dr. Smith and an older version of Will who has his own agenda.
Faced with treachery, a giant spider-hybrid Smith reveals a plan to eradicate the rest of the Robinson family and take over Earth. In a fierce confrontation, Professor Robinson must fight against this monstrous foe, utilizing a dagger crafted by the younger Will. After an intense struggle, they manage to defeat Spider Smith, but not before the unstable planet begins to tear itself apart.
As they scramble to escape, they face dire odds, including losing the Jupiter 2 to an explosive force. However, in an unexpected act of love and bravery, the future Will rewires the time machine to help save his father, which ultimately allows the family to escape the collapsing planet. They bravely navigate through the planet's core, using the planet's gravity to propel themselves back to safety. The family embarks on a final jump into hyperspace, setting their course for Alpha Prime, hopeful for a new beginning.
