Mala (Evan Rachel Wood) and her friend Senn (Justin Long) are young alien creatures who live on Terra, a planet from a star system in the Milky Way. Terra is a peaceful planet of alien creatures who have a rich semi-advanced culture.
One day a large, mysterious object blocks the Terrian sun, piquing the Terrians' interest. However, since the Terrian culture bans the development of new technologies, such as telescopes, without the approval of the ruling council, none of the inhabitants are able to get a closer look at the huge object in their sky.
Mala, who is inventive and headstrong, goes against the rules of her community and creates a telescope, which she takes out into the dark empty area outside the Terrian city and uses to view the object and witnesses smaller objects coming from the large object that turn out to be incoming scout spaceships. She returns to the city to find that the scout spaceships have already started abducting Terrians (who willingly offer themselves to the scout spaceships mistaking them as their new "gods").
After Mala's own father, Roven (Dennis Quaid) is abducted she goads a ship into tailing her and lures it into a trap, which causes it to crash. Afterward, she saves the life of the pilot, revealed to be a human, an officer named Lieutenant Jim Stanton (Luke Wilson). After his personal robot assistant named Giddy (David Cross) warns Mala that Stanton will die without a supply of oxygen (which the Terrian atmosphere does not contain), she creates an oxygen generator and fills a tent with air containing oxygen so that Jim can breathe, and eventually convinces Giddy to teach her human language. The Robot informs Mala that the mysterious object is a generation ship called The Ark, containing humans from Earth.
Centuries beforehand, both Mars and Venus were terraformed by humans and colonized. But 200 years later, the two planets demanded independence from Earth, which the Earth government refused to grant them due to the high demand of resources from the two colonies. The dispute between the three planets escalated into a violent interplanetary war that left all three planets uninhabitable. The Ark, containing the remnants of the human race, traveled for several generations looking for a new home. When Stanton awakes the robot informs Stanton and Mala that a crucial part of the ship was damaged in the crash, so Mala offers to make a replacement part herself. When Stanton, Mala, and the robot return to the crash site, they discover that the ship has been moved.
The trio track the ship to a huge underground military facility which had been built by a previous, warlike generation of the Terrians. The trio realizes that despite the current peaceful nature of the Terrian city, the elders have secretly retained the military technology from the dark days of war. After infiltrating the facility, fixing the ship and flying back to the Ark, Jim orders Mala to stay and goes to be debriefed.
Mala ventures off and finds Roven, but before she can rescue him, the human guards are alerted to her presence. While trying to save Mala, Roven kills himself and two men after breaching the hull, and she is captured, but Stanton helps her to escape back to Terra. The commander of the military wing of the Ark, General Hemmer (Brian Cox), takes power over the civilian leaders in a coup, and declares war on Terra, citing the deteriorating condition of the Ark. His goal is to annihilate the Terrians so that the humans can turn Terra into the new Earth. He plans to drop a huge machine onto the planet's surfaceâcalled the Terraformerâwhich will create an Earth-like atmosphere. Stanton is sent to be in the first group of space-fighters designated to defend the Terraformer, while General Hemmer will go down to the planet's surface in the Terraformer to personally supervise the terraforming process.
After the humans drop the Terraformer machine onto the surface, it begins to replace the native gases with oxygen and nitrogen, which will asphyxiate the aliens. The terrian elders bring out all of the secretly-hidden military technologies from their secret base, and huge waves of Terrian glider-fighters attack the Terraformer machine. The human spacefighter ships begin a huge and bloody battle against the high-tech alien glider-fighters, and the sky is filled with laser cannon fire and explosions.
Finally, as the Terraformer is close to completing its terraforming objective, Lieutenant Stanton realizes that annihilating all Terrians is morally wrong. He turns his ship towards the Terraformer machine and attacks it. As his ship is raked with anti-aircraft defensive fire, Stanton fires his air-to-air missiles at the Terraformer's command module, destroying it, and killing General Hemmer. His ship is destroyed in the resulting explosion. Knowing that he has done a good deed, he accepts his fate and dies calm and serene.
An epilogue shows what happened in Terra some time later. The Terrians and the humans have decided to live in peace. With the Terraformer machine destroyed, the Terrian atmosphere becomes safe once again for the aliens. The Terrians create a sanctuary for the human colonists to live in, with an Earth-like atmosphere. In the human sanctuary, a large statue of Lieutenant Stanton is erected, in honor of his memory and sacrifice.
What had been built by a previous, warlike generation of the Terrians?
huge underground military facility