On the planet Terra, a civilization of floating tadpole type creatures live a peaceful existence, pretty much blindly following the teachings and rules laid out by the Elders, including Doron (voice of JAMES GARNER). That is, except for teenager Mala (voice of EVAN RACHEL WOOD) who lives with her dad, Roven (voice of DENNIS QUAID), but prefers zipping around on high adventures with her friend Senn (voice of JUSTIN LONG) when not questioning authority.
She and the others have bigger concerns, however, when a giant spaceship arrives and blocks out the sun. The others are initially entranced by the sight, wondering if it's some sort of god, but the notion is quickly squashed when fighter ships quickly descend into the Terran village, blasting away at the inhabitants when not abducting others, such as Roven.
Seeing that happen, Mala engages one such ship, trying to get it to take her, but her actions result in it crashing. When she goes to investigate, she discovers human Jim Stanton (voice of LUKE WILSON) and his trusty robotic assistant, Giddy (voice of DAVID CROSS). Informed that the Earthling will die if he isn't given breathable air, the resourceful teen invent an oxygen tent of sorts and saves his life.
It turns out he's a military pilot, like his brother Stewart (voice of CHRIS EVANS), who's arrived on Terra under the orders of General Hemmer (voice of BRIAN COX) to make it their new home. It turns out Earth as well as colonies on Mars and Venus where destroyed in the past, and the small assembly of survivors on a spaceship-based ark of sorts are all that's left of humanity.
While the Council wants to see if the two groups can peacefully coexist, Hemmer -- based on his militaristic leanings and knowledge that their ship's air is running out -- would rather just wipe out the Terrans and claim their planet. And he intends to use an oxygen generating machine -- that will create a breathable atmosphere for the humans but consequently kill all of the Terrans -- to do the deed.
With Jim -- through his interaction with Mala -- realizing that's the wrong decision, he decides he must do what he can to stop the deadly invasion, all as the peaceful Terrans reveal that they have a secret past they intend to use to defend their planet.