In 2077, the world is a shadow of its former self, ravaged by the conflict against a race of alien invaders known as Scavengers (or "Scavs"). Among the few remnants of humanity, Tech 49 Jack Harper (Tom Cruise) finds himself as one of the last drone repairmen stationed on Earth. Devastation was wrought upon the planet sixty years earlier when the Scavs destroyed the moon, unleashing catastrophic earthquakes and tsunamis. Although the invaders were ultimately defeated through the use of nuclear weapons, the aftermath left Earth mostly irradiated and uninhabitable. The few survivors fled to a colony on Titan, which is powered by energy harvested from the sea by massive oceanic power stations.
From their base, Tower 49, perched over the remains of northeastern United States, Jack operates alongside his partner and lover Victoria "Vika" Olsen (Andrea Riseborough). They are tasked with maintaining the autonomous drones responsible for protecting the power stations from the lingering threat of Scav bandits. Their orders come from Sally (Melissa Leo), their mission commander located on the colossal tetrahedral space station known as the Tet that orbits Earth. With plans to join other survivors on Titan in merely two weeks, Jack and Vika lead a routine existence. However, Jack is haunted by recurring dreams of a mysterious woman at the Empire State Building before the war struck, a time prior to his existence. Moreover, he has kept a secret forest hideaway he occasionally visits.
The monotony of their life is disrupted when a Scav signal beacon leads to the crash of an American spacecraft. Despite Jack’s orders for the drones to stand down, they attack and kill most of the sleeping crew. In a moment of instinct, Jack saves a woman named Julia (Olga Kurylenko), identifying her as the figure from his dreams. Julia clarifies that she was part of a NASA mission, but refrains from sharing further details. Together, they venture back to the crash site for the ship's flight recorder, only to be captured by Scavs, who are revealed to be living humans hidden underground. Their leader, Malcolm Beech (Morgan Freeman), unveils a shocking truth: the alien invasion was a fabrication. He reveals that the drones serve the alien intelligence and are programmed to eliminate human life. Beech's goal is to utilize the Odyssey's nuclear reactor to create a bomb aimed at destroying the alien command center, the Tet. He demands Jack reprogram a captured drone to carry out this audacious plan.
Upon their return journey to Tower 49, Jack and Julia find themselves at the ruins of the Empire State Building, where Julia discloses her true identity as Jack's wife from before the calamity. Memories resurface about their past, including the day he proposed. Observing from her video feed, Vika witnesses their intimate moment and upon their return denies them access to the tower, declaring she can no longer work effectively with Jack. This prompts Sally to activate a drone that kills Vika. In a twist of fate, Julia saves Jack from the same drone, and they flee in Jack's ship, pursued by the relentless machines. Their escape lands them in the treacherous radiation zone, confronting Tech 52, a clone of Jack himself. A battle ensues, but upon seeing Julia, the clone begins to experience disjointed memories. After subduing Tech 52, Jack discovers that Julia sustained severe injuries during the conflict.
Impersonating Tech 52, Jack steers his way back to Tower 52, where he encounters a clone of Vika and snatches a medical kit to tend to Julia's wounds. The shocking revelations do not end there; upon confiding in Beech, Jack learns the full extent of the deception: the Tet is a ruthless artificial intelligence that has enslaved Earth for its resources while using clones of Jack and Vika to control the drones. Deciding to take a stand, Jack resolves to reprogram the stolen drone to obliterate the Tet. As they make their exit from the underground stronghold with their high-stakes mission in hand, they're ambushed by more drones. The ensuing chaos sees Jack and the team manage to fend off the drones but forces them to reconsider their means of delivering the nuclear payload.
Jack offers to be the one to deliver the bomb himself, with Julia devising a plan to accompany him to maintain the ruse that Sally had insisted upon. During their flight, Jack accesses the Odyssey's flight recorder, unveiling the tragic history of how they became intertwined in this human struggle against the Tet. Memories flood back as he learns they were once pilots on the Odyssey mission re-directed when the Tet was discovered. The realization strikes home just before Jack confronts the Tet’s embodiment of Sally, where he inadvertently unleashes the truth contained within the sleeping capsules. Together with Beech, Jack triggers the nuclear bomb, leading to the demise of the Tet at their own expense. In the aftermath, the destruction unleashes a wave of freedom, neutralizing the remaining drones just moments away from slaughtering the surviving humans at the underground base.
Three years later, Julia has carved a new life for herself and her young daughter in the recovering wilderness of Earth. When a group of survivors arrives, a figure emerges from the crowd—Tech 52. His voice-over reveals how their previous encounter reawakened his memories of Julia, setting him on a quest to find her once more. Sharing the same past as Jack Harper, he steps forward to reunite with "his" family, embodying hope for the future amid the ruins of a once-great civilization.
