Jack enjoys some 'down time' in his secret spot near the lake, when he awakes to see a spaceship falling to earth. He hurries out to the wreckage - and finds humans in space-pods, in a deep sleep. Suddenly one of the drones shows up and starts to kill the humans - and Jack can't do anything about it. At this point he discovers that in one of the pods is the woman from his dreams - and saves her life by using himself as a shield.
He takes the pod back up to his mid-air Tower where the woman, Julia, is revived. Vicky tells Sally, who instructs Jack to bring her up to the Tet in space.
Next morning, Julia convinces Jack to take her back to the crashed ship to find the blackbox. While there, Scavs surround them and Jack is knocked unconscious.
Jack is woken by Beech (Morgan Freeman) who tells him the truth -- the Scavs are not aliens, but the humans who have been left behind and fought against the aliens, who are the ones who brought the Tet to Earth and are not draining it of its resources. They ask for Jack's help to reprogram a drone, to send it back up to the Tet and destroy it.
Jack thinks about it. He leaves with Julia to go to the Empire State Building where he can signal Vicky. She watches the spaceship return for them, where Jack and Julia steal a kiss. Vicky is heart broken, and tells Sally they are no longer an effective team. Sally sends in a fail-safe - a drone that kills Vicky. Julia manages to shoot it down.
They escape but are chased by drones. They shoot a few down, but are bumped into the radiation zone and crash land. Jack soon realizes he's been lied to - and things get worse when another Jack Harper shows up to fix another idle drone. Jack fights with the other clone (Jack '52), and steals his spaceship.
Julia has been injured, but Jack manages to get a medi-kit from another Vicky in another tower, and saves her life. They return to the Scavs and Jack decides to take the mission ... but more drones show up and start to kill the humans. They destroy the drones too late, and Beech has been wounded and most of the humans killed.
Jack decides to take the explosive fuel cells in person with Julia in her sleep pod. On the way he listens to the black box to learn about his journey -- Jack, Victoria, Julia and the others in the downed spaceship were on a mission from Earth to confront the Tet that had arrived in Earth's atmosphere ... when the Tet began to pull them in. Jack jettisoned the others, but Jack and Victoria were taken captive and cloned.
Sally is quite sharp, and knows that Jack is lying. But rather than taking him out, she allows him to get nearer until finally he can approach closer to a pyramid that seems to be the alien mind. The pod is opened, and Beech climbs out. Sally calls in some drones, but not before Jack detonates the fuel cells.
Julia wakes up back on Earth in Jack's secret spot to see the Tet explode.
Several years later she has a daughter, somehow, and still hasn't left the little hit when several human survivors, led by Jack 52, find her.