The movie opens with a peaceful look at the world of Terra, inhabited by a strange but peaceful breed of floating creature with big eyes. They go about their usual day in their vine-strewn village, with a sick child seeing a doctor and students attending an outdoor class. As the teacher does a roll call, she notices two students that are absent -- Mala and Senn.
Mala and Senn are ditching school, flying above a cloud-covered part of Terra in built hovering vehicles. Mala challenges Senn to a race, but he kiddingly accuses her of cheating. She denies it, but not before activating more propellers on her craft. The two begin flying into a cavern, with Senn pulling up when he notices a wind tunnel. Mala is suddenly sucked into it, but Senn rescues her using the anchor on his craft. Senn insists they go home shortly after, but Mala flies to the border of a forbidden zone, marked off by statues with their hands raised in the air. She suddenly stops when she sees a large shadow leaving its mark over the world. It soon engulfs the whole planet side of Terra, including Mala's village. Everyone rushes inside, and vessels begin flying through the area, telling everyone to calm down.
Back at her house, Mala is eating dinner with her father. They accidentally set out a third plate for a missing member of the family, the mother (who is obviously no longer with them, as the dad stares over at a threesome of statues, sighing). Mala comes up with the idea of building a telescope to get a closer look at the huge machine blocking out the sun, but her father forbids it, saying new inventions are not accepted without approval from the elders. She persists, and he sends her to her room.
As her father sleeps, Mala goes ahead and builds the telescope anyway, then proceeds to a high point in the village. She looks through it and notices the big thing blocking the planet's light is actually a huge, complex spacecraft -- and smaller spacecraft are flying out of it! They begin flying towards the village, where they capture Terra members. Some willingly offer themselves, thinking that the machine is a new God for their planet. Mala's father awakens and flies outside when he notices that she's missing. Mala returns to the village, only to see her father get captured by one of the spacecraft. She willingly makes herself available for capture, but the spacecraft simply flies past her. She refuses to give up that easily and gets her flight machine back, forcing one of the ships to pursue her. She flies down into the same canyon where she and Senn were before; forcing the ship into the wind tunnel and making it crash into a snow bank below. She lands her craft to get a closer look at the ship, and out of it bursts a man in a space suit.
He collapses to the ground when he realizes that the air isn't exactly breathable. His mask pops open to reveal the face of a human, Jim Stanton. He gets a glimpse of Mala before he passes out, and a depleted oxygen mask latches onto his mouth. Mala, not sure what's going on, begins to drag Jim back to her ship, while something watches in the distance through a red display.
Mala successfully sneaks Jim into her home, but just when she's about to examine what he is exactly, she's interrupted by a robotic voice. It's the voice of Giddy, a robot assistant to a visiting Earth military force. He explains that Jim is dying and cannot survive on the planet's atmospheric conditions, and that he needs something called oxygen. He guides Mala on how to build him a temporary oxygen tent, using plant life she has gathered around her house. She successfully builds the tent, just as Jim's oxygen supply runs out. He breathes the air and avoids suffocation. While he's passed out, Giddy helps Mala learn the English language of Jim's human race, with just a few seconds of looking into her eyes with a data feed.
Jim comes to, wondering just what Mala is. She explains that Giddy taught her the human language, and Jim chastises the robot, saying it's against his command. Giddy explains he was dying and thought Mala could help. Just then, more of Jim's fellow soldiers come flying through. He believes they're looking for him and bursts out of the oxygen tent. He hangs by the doorway of Mala's house, but his lack of oxygen forces him to pass out and fall down the side of the vine. Giddy and Mala swoop down and grab him, just before he can impale himself on sharp vines below. They bring him back into the house, without any fellow Terrans noticing.
Giddy explains why Jim and the others are around Terra to begin with. They explain that they've lived on Earth successfully for many years, only to deplete the planet's natural resources over time. They build colonies on two separate planets to keep things going. However, the colonies were seeking independence, and war soon broke out afterward. As a result, all three planets were destroyed, and the remaining humans have been seeking out another place to live ever since.
Jim awakens to find a globe structure of some sort that Mala put together for him. He's amazed at the work she did with the gears, but she says it was nothing. He figures that she's got the know-how that would help him repair his ship. She's reluctant, but eventually makes a deal if she can rescue her father in the process, now in the captivity of his military team. They agree.
Senn drops by, and Mala tries to brush him off so he won't discover Jim. Jim, wearing his rebuilt oxygen tank, attempts to choke him. Mala stops him, and she tries to explain to Senn what he's doing there. Senn runs off in fear, and runs to the elders to tell them that Jim is there. Jim, Mala and Giddy successfully escape, but not before Mala gives Senn a glance, as if he's betrayed her in some way. Senn is somewhat heartbroken by this.
As Mala flies Giddy and Jim to the ship in their cruiser, bombs begin dropping in the Terra village, destroying several structures. Jim tries to stop the bombs by waving to his cruisers, but they don't see him. Mala is distraught by all the destruction that's happening.
The trio makes it down to where the ship was, but it's not there anymore. Giddy is able to track the path of where the ship was taken, and they walk to some sort of structure in the snow. They sneak inside and hitch a ride on a moving platform, and see the ship. However, before they can devise a plan, Terra guards surround them. Acting on a whim, Jim pretends to take Mala hostage and gets her to the ship, while Giddy makes the repairs with gears that she built. The trio makes it inside the cockpit and try to start the ship as bigger Terra spider walkers approach, firing guns. The ship successfully starts, and the trio flies off into the reaches of space, close to the huge mechanical structure the Earthlings came in.
Jim asks for clearance to land, but not before seeing part of the Ark (the ship) blow up from malfunction. This frustrates Jim. He lands the ship and tells Mala to stay put, and that he'll be back to take her to her father. Giddy goes with him while Mala frustratingly sits.
While a machine examines Jim, it asks how he managed to survive and who helped him. He explains that a local did, and although they had weapons, they didn't use them. Meanwhile, in a room upstairs, General Hemmer, the leader of the military faction of the surviving humans, is explaining why he thinks that they should perform a hostile takeover on Terra now. It's a fully livable planet, and humans are running out of time. The President, however, feels that a hostile takeover isn't the answer, and to hold off on the plan. Hemmer is clearly not happy about this.
Mala, growing impatient with waiting on the ship, puts on a mask and, wielding a gun, starts to sneak around the ship. She thinks she sees Giddy for a minute, but it's just one of many service droids on the ship. She continues to look around.
Hemmer meets up with Jim and a fellow pilot, who happens to be his brother. He's proud of what he's done for his country, and asks questions about the Terra species. He asks if they can possibly fight, and Jim explains that they have weapons, but they're mostly peaceful. Hemmer sees this as an advantage, as they can die with honor. Unsure of what that means, Jim begins to question his loyalty to Hemmer. His brother's no help, as he feels serving under Hemmer's command is an unquestionable order.
Mala makes her way into a room where her fellow Terrans are being detained. Some of them are lying on gurneys, but others are trapped in bubbles overhead. She heads off to another room, with a coal fireplace in the middle of it, and finds her father. She tries to push him out of the room as he comes to, but a pair of soldiers race in to corner them. Her father explains that he loves her, and throws her into another room as the door closes. He grabs a gun and fires at the soldier, inadvertently hitting an air lock. The three of them are sucked into space, and Mala is horrified as she watches her father leave. She falls to the ground, not noticing the pair of guards that walk in to her room.
Hemmer shows the footage of the coal room attack to try and convince the Council that the Terrans are a violent race. The President still isn't buying it, and says they need more time to try and figure things out. Fed up with the Council, Hemmer initiates a hostile takeover with armed soldiers on each floor, and says he's dissolving the Council. With that, he approaches Jim and says he'd like him to head up the assault team to take over Terra. Jim refuses after hearing what Hemmer has in mind, but Hemmer tries to explain what's going on.
It turns out the Ark they're on only has a couple of weeks worth of oxygen left, and after that, the humans will die. He then turns off the holographic display to reveal Mala in a room, via a two-way mirror. She's able to breathe her own air with the environmental set-up in the room, and Hemmer, putting Jim under restraint, drops his brother, Stewart, into the room. Stewart begins suffocating as Mala tries to help him. Hemmer presents Jim with a button that will pump oxygen into the room to save Stewart, but will suffocate Mala. He has to make a choice. Jim, not wanting to see his brother die, presses it. Stewart survives, but Mala begins to run out of air. Jim looks over at Giddy and orders him to save Mala. Giddy grabs a mask for Mala and cuts through the glass using his lasers. The room explodes from the pressure, and Giddy helps Mala get out, but not before she sees Jim, noticing that his hand had been on the button.
The two escape in Jim's ship, but not before a bunch of missiles plow into it, sending it crashing down to the planet side of Terra below. Mala ejects successfully, and tries to hand on to Giddy to avoid crash-landing, but falls to the ground anyway. She's discovered and picked up by a Terran craft.
She awakens to find Senn standing there. Senn apologizes for what he did to Mala earlier and they make up. She asks to see Giddy, but the elder informs her that he's been taken into captivity following their landing. She asks to see him. They take her to an underground part of the city, where the elder explains that this is part of Terra's past, as well as its future, to keep it alive. There are several warships about, including vessels armed with lasers. She gets to a room where Giddy's becoming annoyed by a pair of Terrans trying to torture him with electric prods. She convinces them to stop and asks Giddy for help. He refuses to betray the humans, but Mala explains that Jim gave him an order to keep Mala safe, no matter what. After Giddy takes a moment to compute this, he agrees.
Back on the Ark, Hemmer forcibly enlists Jim and Stewart into the first battle wave on Terra. He then explains a battle plan involving a Terraformer, which would convert Terra's current air supply with oxygen. The plan is explained by Giddy to the Terrans as well, and both sides prepare for a fight. Jim takes a moment to figure out what he's going to do, and then joins the rest of the team in their ships.
Senn and Mala, along with Giddy, take to their advanced flying crafts and join in the first battle wave. The first league of human ships come down, and the two sides engage in a gigantic missile-filled, laser-blasting fight with ships exploding everywhere. While this is happening, Hemmer and his crew fly down in the Terraformer, which successfully perches in the middle of Terra's planet surface. It slowly begins pumping oxygen into the air, which in turn starts to suffocate the Terra species. Terra soldiers fire off lasers that damage some of the hoses, but Hemmer, growing impatient, insists that the power be pushed up and rerouted to the working pipes. As the Terrans keep damaging the Terraformer, Hemmer calls for back up. Several more ships fly down to the surface, leveling some of the Terran spacecraft.
Senn's ship is shot, and he flies down to the surface below out of control. Mala thinks he's dead and pursues the ship, not realizing that it's Stewart, the human she was trapped in the room with earlier. As she's firing lasers at him, Stewart asks for back up, and Jim starts to fly in. He notices that both parties are involved, and finds himself facing them both with the Terraformer nearby. He takes a quick moment to think, and then sees the Terraformer. Suddenly, he begins flying straight at it. Hemmer can't believe it. Jim fires all of his weapons, which in turn destroys the Terraformer's main hull -- killing Hemmer alongside with it. In the same blast, however, Jim's ship blows up, taking him with it. Mala and Stewart are both in shock. The oxygen depletes from the planet surface, and the Terra residents are saved.
Mala lands her ship, only to find that Senn is safe with the elder and the others. They embrace. They notice the humans are flying about in a scattered manner, and she's sad because now they have no place to go. The elder tells her that there are alternatives available for them.
The scene now changes back to Mala and Senn, once again flying their makeshift hover mobiles above the city. They're about to engage in a race when Stewart, in his spaceship, flies between them, saluting them. The three of them fly on to a huge covered facility, where the humans have taken refuge on Terra. Stewart flies inside as Senn and Mala fly overhead. Mala then notices a huge statue that's being built in the middle of the facility -- one modeled after Jim. The movie then ends with a fly-over of the planet Terra, now back at peace.
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