In a brief flashback, the main character Luna is shown as a young girl being pushed into an escape capsule by her father, who is then killed in an explosion. Several years later, Luna is preparing for her first day at a school she is transferring into. Upon entering the grounds, she is stopped and scolded by the student council president Menori for running on the pavement, but quickly befriends a kinder girl named Sharla. On their way to class, the girls run into a student named Howard and his gang taunting an older boy from Pluto named Bell, telling him to clean their shoes better. Luna attempts to intervene, only to be told that Bell in fact wants to clean their shoes. At the start of class, Luna is introduced, as is another recent transfer student named Shingo. The teacher discusses a field trip coming up, meant to give the students experience in planetary settling, and some of Earth's late history is revealed. During gym class, Luna, Sharla and another student named Kaoru play Air Basketball against Howard and two others. Luna scores with some help from Kaoru, despite Howard playing rough. On the way home, Shingo nearly hits the girls on a gasoline-powered scooter he has built. While discussing the scooter, they hear Howard and his gang starting a fight with Kaoru. Luna tries to stop the fight, but a member of Howard's gang accidentally starts a fire. Howard and his gang retreats, but Sharla is trapped by the fire.
Luna tries to help Sharla, but ends up getting trapped by the fire as well. Shingo tries to save them in a construction vehicle, while Kaoru helps from the shadows by throwing them a line. They manage to escape, but the incident has been kept out of the media because of Howard's father's influence. A week later, Chako, Luna's robot pet, sneaks into her backpack as she heads for the shuttle to depart on the class's field trip. Before boarding the shuttle, Menori announces the groups into which the class has been divided, with Luna being grouped with Menori, Sharla, Bell, Howard, Shingo, and Kaoru. The shuttle runs into an unusually strong gravity storm, and the captain orders the passengers into escape shuttles as a precaution while they perform an emergency warp to escape it. Howard and Shingo excitedly sit in the pilot seats, but as the shuttle begins to warp, someone's hand inadvertently hits the release button of their group's shuttle, leaving the shuttle and the seven children behind in the gravity storm as the main ship warps away.
The shuttle is sucked into the gravity storm, and thrown out of the far end, in an unknown location far from the colony. The children struggle with the ship's unhelpful computer system to determine their position, and it announces that they have entered the gravity well of a planet. As the children theorize on what planet it might be, Chako emerges from Luna's backpack. With the shuttle's autopilot system damaged in the storm, Chako connects to the computer and guides Luna - who has previous experience flying an escape shuttle - through the procedures to land the ship. The ship is struck by lightning on the way down, and crash-lands into an ocean, coming to rest on a large rock. The next morning, as the children emerge from the shuttle to look around, they are surprised to see real clouds, a real ocean, and a real sun. Chako tells them that the atmosphere is similar to Earth's, though not exactly the same. As the children search the shuttle for supplies, Shingo finds a small inflatable life raft, and Menori and Howard decide to row towards nearby land to scout. On their way, they are attacked by a large snake-like sea monster.
Menori and Howard try to row back to the shuttle, but the sea monster catches up with them. The monster destroys the boat, but Menori and Howard manage to get back to the shuttle. The children hide inside the shuttle until the monster loses interest and leaves. After waiting some time for the tide to rise, the children emerge and try to push the shuttle lose from the rocks where it is caught so that they can float it to land on the ocean currents. They almost push it free, but the sea monster returns. The children quickly hide inside the shuttle, but this time the monster is more persistent, ramming the shuttle repeatedly and eventually forcing the hatch open. It nearly catches Bell in its jaws, but Kaoru throws a knife at its eye and the monster retreats. The force of the snake pulling its head out of the shuttle lifts it off the rocks, and the shuttle slowly floats towards land. The wounded monster returns once more, but by then the shuttle has entered water too shallow for it to follow. The children tie the shuttle to a tree so that it cannot float away again, and spend the night in the shuttle. Early the next morning, the ground shakes from what sounds like large footsteps.
The children hear the sounds of a large creature outside the shuttle, and Sharla catches a glimpse of it out the window, causing her to start crying hysterically. The creature bashes the shuttle repeatedly, but after making no progress, seems to lose interest and leaves. In the morning, they find a large footprint in the shuttle's hull, and Chako estimates its height to be around ten meters. Chako deems the shuttle's flight systems useless, but Shingo says he might be able to fix the communications system. They take inventory of what they have with them, and then split up to search for food and water along the beach, with Shingo and Chako staying behind to look at the communications system. Luna tries to cheer Sharla up, but she's very shaken over the recent events, and depressed with their situation in general. Luna and Sharla find some fruit, but a strange carnivorous pitcher plant catches them in its vine-like tentacles. Hearing Sharla scream, Bell and Kaoru come to their rescue, and destroy the plant's pitcher. Shingo doesn't have much success with the communications system and Chako is low on power. The group returns to the shuttle for the night and eat the fruit that Luna, Sharla, Bell, and Kaoru bring back, and Chako uses it to recharge her fuel cell.
The next day, the children set out again to find food and water, this time with Shingo and Chako going as well. Kaoru is told to go with Shingo and Chako, but is reluctant, and eventually goes off on his own after finding some fruit. At the beach, he finds some obsidian. Bell and Sharla attempt to start a fire, first trying to get a spark from rocks, and then by spinning a stick with their hands. Bell tries until his hands are blistered and bleeding, but insists that he must continue, despite Sharla's pleading. Luna, Menori, and Howard head into the forest. First chasing after a small kangaroo-like creature, they then encounter a giant lizard that chases after them instead. They get away at first, but lose their bearings. While trying to find their way, they find a large fresh water lake, but the lizard catches up with them. The three climb up a very large tree to avoid it, but it is soon scared off by loud thumping footsteps. As the source of the footsteps emerges from the forest, it is revealed to be an elephantine creature with a long prehensile tongue that tries to reach the leaves of the big tree to eat, but it cannot. Howard gets frightened and screams, scaring the creature away. Menori and Luna resolve to climb a small mountain in the distance to re-establish their bearings, even though it will mean they won't make it back to the shuttle by nightfall, and Howard follows.
Kaoru fashions the obsidian he found into a crude spear which he uses to catch a fish. Chako and Shingo collect worms for bait and build simple fishing rods, but don't have much luck catching fish without hooks. Bell and Sharla continue their attempts to build a fire together, and Sharla eventually succeeds shortly before sunset due to her lighter touch and faster hands, despite both of them rubbing their palms raw. The group is concerned that Luna, Menori, and Howard have not returned, and vow to search for them at sunrise. They are also impressed at the obsidian knife and spear-head that Kaoru made, but he insists that the others should make their own. When Bell reveals that the fish should be cleaned and gutted before eating, something that Kaoru didn't know, he realizes that they all need to work together, and makes more knives, and a fishing hook out of bone for Shingo and Chako. The next day, after spending a night in a small cave, Luna, Menori, and Howard reach the top of the mountain, and discover that they are on an island. Despite being at first depressed that there are no people in sight, they are able to find their bearings again. After drawing a map of the island, they return to the lake for more water, then set off for the shuttle again, meeting up with the other children who have started searching for them.
The children now have sources of food and water, but the three-hour round trip to the lake takes up too much time and energy every day, and their only means of carrying water are the plastic bottles from the shuttle's emergency rations, which don't hold much water. Bell and Shingo come up with the idea of digging a pit and filling it with water, using their deflated life raft - which washed up on the beach during the night - to hold and carry the water. After digging the pit, the children head towards the lake, on the way encountering the small kangaroo-like creature from earlier. Sharla finds it cute, and calls it a tobihane, from the verb meaning "to hop" (飛び跳ねる tobihaneru?), but she is horrified when the others want to catch it for food. They reach the lake, which Sharla names "Fairy Lake", and stop to rest. When Howard pushes Luna into the lake, she suddenly feels a strange sensation, and is briefly surrounded by a pink glow. After they find fruit on the trees and fish in the lake, Shingo suggests the idea of building a house in the big tree, which Sharla names "Magnificent Tree" (大いなる木 Ooinaru Ki?). As the children inspect the tree, Menori realizes that the footprints left by the elephantine creature they'd encountered earlier were the same as the footprints left in the shuttle's hull after their first night on land. They decide the area around the tree is simply too dangerous, and head back to the beach with the raft filled with water. On the way back, Shingo slips and accidentally spills some water, and Menori's overly-strict admonishment is questioned by Luna.
Long days of little food followed by long nights of little sleep in the shuttle's seats are beginning to take their toll on the children, who are starting to get irritable and snappish with one another. Luna once again raises the idea of moving to Fairy Lake, building a house in the Magnificent Tree to keep it out of reach of the giant lizard. The children survey the tree, leaving Kaoru behind to tend the fire, who makes saws from panels scavenged from the shuttle. Chako, Shingo and Howard measure the tree for size and strength. When they return to the shuttle, Howard takes a small branch of the Magnificent Tree with him as a souvenir. Shingo and Chako spend the night drawing up plans for a house. The next day, the children - sans Howard, left behind to tend the fire and catch fish for dinner - find straight, sturdy trees and vines to construct the foundation of the house. Dismayed by the amount of effort required, and despite some mishaps, the group manages to complete the foundation. Bored of not being able to catch any fish, Howard comes to see how they are going, but when he climbs the tree to test the foundation, the whole structure collapses. Disheartened, they return to the shuttle - only to find that it too has been destroyed, and their fire has gone out.
In the destroyed shuttle, Menori finds her violin undamaged in one of the storage lockers. Luna sees the large creature's footprints leading away. Bell manages to re-start the fire from the remaining embers, and the children spend the night in a nearby cave. Luna decides that their only remaining option is to build a house in the Magnificent Tree after all. She comes up with the idea of using the shuttle's broken-off wings for the house's foundation and floor, but Menori quickly points out that the wings simply too heavy for them to move. However, Shingo comes up with ideas for some of the smaller components, such as making pulleys, or using a porthole for a window. The children return to the lake and start to search for more building materials and food, but while Luna is tying a pulley to a branch the huge creature returns, in a frenzy. Luna falls onto its back, and it runs into the lake. Suddenly, she starts to glow pink, and sees the creature's memory of Howard's Magnificent Tree branch, which he'd brought back to the shuttle the previous day, lying in the shuttle's open hatchway. She realizes the creature had been injured trying to reach the branch, and finds a piece of the shuttle sticking out of the side of its neck - when she pulls it out, the creature calms and starts to eat leaves. However, Howard, returning with fish, sees it and screams in terror, which frightens the creature away.
The children, with Pague's help, rip some of the remaining bulkhead panels off the shuttle to use on the house, while Menori stands to one side directing their efforts. As they start to lift the panels onto a cart for Pague to haul to Fairy Lake, Howard protests that Menori is standing doing nothing. Luna asks Menori to pitch in, but on helping to lift the first panel, she cuts her finger. As she spaces out, Bell fashions a bandage from a strip of Sharla's handkerchief. She has a flashback to a memory of her mother taking away her pain when she injured her finger as a child, then a memory of her mother's funeral, with a voice-over from her father commanding her to always hide her emotions from other people. Sharla and Shingo attempt to cheer her up, but she brushes them off.
As children put some finishing touches on their house, Howard emerges from the forest, leading Bell, who is bowed under the weight of one of the shuttle's seats, intended for Howard's exclusive use. Luna protests that if Howard wants the seat, he should carry it himself. They declare the house almost complete, lacking only a front door, until Menori suggests a shower. Meanwhile, Kaoru works at narrowing a river with rocks to force the fish into a smaller area, but still finds them difficult to catch with his spear. While the other children collect wood to construct a shower room and leaves for shower curtains, Bell and Luna attack a pitcher plant, using logs to occupy the tentacle vines. They miss one, which catches Luna. Bell saves Luna, but berates himself for missing it. Luna tells him to have more confidence in himself. They return with the pitcher to use as a tank for the shower. That night, as Bell muses by the fire, Sharla comes to remind him of all the good things he's done for them.
Two weeks later, the children have returned their efforts to food-gathering, but they find they've already picked the nearby trees clean of fruit. They decide to go further afield the next day, but all are concerned about Kaoru's habit of doing his own thing. The following day, Bell, Luna and Chako find potatoes, while Kaoru and Sharla check the fish trap, but find it empty. Kaoru walks away to hunt on his own, but Sharla turns back to see fish swim into the trap. Kaoru arrives to dinner late, having caught a small lizard while hunting. Later that night, Luna brings Kaoru dinner as he sharpens his knife in the cleaning area, and she tells him that he doesn't have to act alone - they're stronger if they work together.
After stopping work for the day, Luna goes to wash her hands in the lake. As she remembers the other times she saw strange visions while in the lake, she suddenly sees a vision showing a journey down a river into the Eastern Forest, and a voice telling her to come. That night, she tells the others about her desire to go there, and Howard and Bell volunteer to join her. Bell and Luna build a raft out of bamboo, while Howard makes a bow. Shingo and Menori are working the field, until Shingo suddenly collapses. They leave him to rest in the shade of the Magnificent Tree, and he sits starting at a photo of his family.
As Luna, Bell and Howard head deeper into the Eastern Forest, Shingo works on the communication system back at the house, but is frustrated that he doesn't have enough parts. Shingo and Chako return to the shuttle for more parts, but Shingo gets angry at Chako's dismissive attitude. Later, he tries to operate the communications device using Chako as a power supply, but is unsuccessful.
Chako and Shingo investigate the machine, and determine it to be a nano-plant - a collection of nanomachines - that was controlling the crustacean. They realize the nano-plant means there is intelligent life somewhere on the planet. Shingo announces that he might be able to use the nano-plant to fix the communications system, but Howard assumes that Shingo is guaranteed to be successful and gets excited. Despite working all night, Shingo isn't finished by the next morning - Howard, however, continues with his unreasonable expectations. Howard and Shingo get into a heated argument, which ends with Shingo storming off. Luna comes to the conclusion that Shingo is homesick - being two years younger than the rest of the children, he feels it much worse.
The children are forced to put their plans to re-visit the ruins on hold when Luna develops a high fever. On Chako's advice, they split up to search for medicinal foods and plants for her - Chako and Sharla look for an arrowroot-analogue, Bell and Shingo look for mugwort, Kaoru goes to get eggs, Howard looks for fruit, and Menori remains behind to take care of Luna. The hunt for arrowroot is difficult, worsened by the arrival of bad weather, but Sharla insists on continuing, even after badly scraping her knee. Sharla wants to be strong for Luna, so Chako tells her the story of her first meeting with Luna, shortly after her mother died. Chako tells Sharla the secret of Luna's strength - to remember that even when bad things come, there's always a blue sky in your heart.
Shingo, impatient with the delay in plans to investigate the ruins, sneaks out early one morning, talking Howard into coming with him, and Howard kidnaps Chako without Shingo's knowledge. When the other children wake up and find them missing, Luna, Bell and Menori follow. In the forest, Chako and Shingo are fascinated by the fact that gravity seems lower. Both groups find themselves lost and walking in circles. Chako, Shingo and Howard find a giant tobihane, dead, and are subsequently chased by the giant Tasmanian-devil-like predator that killed it. They run into Luna, Bell and Menori, and the six of them flee together. The mysterious voice tells Luna to jump over a cliff to escape, and when the children do so, they disappear half-way down and find themselves in front of the ruins. They realise the forest they were lost in was some sort of illusion. The giant crustacean appears again, but in a reflex, Luna tells it to stop in her mind, and it does. They approach the door of the ruins, and when Luna places her hand against it, the ruins glow pink and the door opens. The children enter, finding a small alien boy in a cold-sleep capsule inside.
The children discuss the boy, and the possibility of first contact with aliens, and Luna remembers the image of the alien family that she'd seen the first time she came to the ruins. Luna looks at the boy in thought, while the other children push random buttons on a nearby console to see what happens. Suddenly, a hologram of the planet appears, showing several locations marked. The planet starts red, but blue areas start spreading from each marked location. In the cold-sleep capsule, the boy suddenly opens his eyes. They all hear the voice that Luna had heard earlier - it says "Alduram Gyet", and when Luna places her hand on the capsule and repeats it, the capsule opens. As the child gets out and stands up, a card comes out of the cold-sleep capsule's control panel. When they take the card, the ruins start shutting down, and the door starts closing. The children escape with the alien boy just in time.
The next day, Howard volunteers to look after the boy - who seems to be unable to speak - in order to get out of doing more strenuous work. Luna thinks Alduram Gyet is the boy's name, but Howard, unable to pronounce it, dubs him Adam. Chako and Shingo study the card from the ruins. Howard attempts to teach Adam how to steal fruit without being caught, but while Howard is distracted, Adam fills his arms with fruit and starts throwing them around. Menori scolds him for wasting food, and Howard accidentally reveals that he was teaching Adam to steal. Adam tries to help the others in their tasks, but whatever he does to help, Menori scolds him for messing up. Later, Menori plays her violin, and Adam sits listening, enthralled. That night, the children try to teach Adam to say their names, but Adam is only interested in Menori. He tries to get her to play her violin, but Menori becomes angry at him for touching it. Menori tells Luna she has no idea what to do with children, but Luna tells her she just needs to smile.
As the weather continues to become colder and more overcast, Luna, Shingo and Chako return to the ruins to investigate it as a warmer place to live, but are unable to find a way in. Chako takes a sample of the substance being emitted from the top, and the three return to Everyone's House. Menori and Howard scavenge the upholstery from the shuttle's seats to make cloaks. Bell, foreseeing colder weather to come, wants everyone to move to a cave. However, despite Bell's enthusiasm for its shape and location, the cave's rocky floor and dank atmosphere don't endear it to any of the other children, who are reluctant to leave the house they worked so hard to build. Bell decides to work on his own.
Two weeks later, the snow lies thick on the ground, but in the cave - named "Star Hole" by Sharla - the children are surviving. Pague is living in a rock shelter nearby, but he is suffering in the cold, and leaves for him to eat are getting scarcer. Bell, Shingo and Chako return to the ruins to find a way in and shut it down, trying to interface the communications system with the card that came from Adam's cold-sleep capsule, but are unsuccessful. On the way back, however, they find a valley full of other creatures like Pague, which is kept warm and fertile by a hot spring.
The snow is falling heavily, and no one is able to find any food. Kaoru decides to head out again, even though it's close to sunset, but falls down a crevasse while chasing a tobihane. When he doesn't return, Luna goes to look for him. She finds him and pulls him out of the crevasse, but the snow is falling too heavily to find their way back to the Star Hole, so they spend the night in a snow cave. Luna brings up the time Sharla found another boy's ID card in Kaoru's clothing. The boy was Louis, Kaoru's rival at pilot school. While Kaoru was piloting a ship through an asteroid field, the hull was punctured and Louis was sucked into space. Kaoru had blamed himself ever since, but Luna, remembering her father's last words, tell Kaoru that perhaps Louis was telling Kaoru to live on.
A blizzard has been going on for ten days, preventing any of the children from leaving the cave. Shingo, Chako and Adam use the opportunity to investigate the card they found in the ruins. They realize the card is a biometric identification system, encoded to respond only to Adam. Bell, Luna, Shingo, Chako and Adam brave the blizzard to head for the ruins. While they stop for the night en route, Adam dreams about his parents. Chako starts shutting down due to the extreme cold, but at her insistence, they press on. They reach the ruins and try to open the door, but Chako collapses. Adam cries out for her, and suddenly the card lifts into the air, glowing green, and the door opens.
Back at Star Hole, Adam has a dream in which he sees his parents in some sort of control room. He sees his mother coughing, then they place him in the cold-sleep capsule, and he awakes with a start. Later, the children discuss the dream. Chako and Shingo believe the ruins are a spaceship, and want to return with Adam to spend several days investigating. Kaoru takes them there, while the rest of the children move back to Everyone's House. Five days pass while Chako and Shingo investigate every nook and cranny in the ruins, and Adam tries to recall the memory of his parents. Adam eventually remembers his mother's last words - "for the sake of the future", and when he speaks them out loud, the walls light up, and the centre of the room's floor lowers down, revealing a hidden door to the control room.
Shingo is able to make contact with the newly-arrived spaceship, the Orion, who reveal that they need a replacement gyrostabilizer, before the radio cuts off as the ship enters the atmosphere. Adam fears that he'll be left behind alone if they get rescued, but LUna promises to take him with them. The children run to the four sides of the island to make signal fires so that the ship can find them. Howard gets the closest one, the eastern end, and starts his fire, Adam, Chako and Shingo stay at the ruins, and the rest of them head west. While waiting to climb the rope up the cliff leading out of the Eastern Forest, Kaoru decides to investigate behind the waterfall, and finds a cave leading up to the top. They then split up to head for the north, west and south extremities of the island.
Kaoru finds the escape pod from the Orion washed up on the shore, and brings the occupant - an old man - to the rest of the children. When the old man wakes, he hurriedly puts out their signal fire, telling them the people on the ship are escaped prisoners. They'd hijacked the ship and killed the rest of the crew, only to be sucked through a gravity storm, finding themselves near the planet, where they picked up Shingo's signal. The old man, named Porte, was the ship's mechanic - he sabotaged the ship as it came in to land, stealing the spare gravity control device before escaping. He also realizes he knows who the children are - their disappearance was big news throughout known space, and Howard's father had offered a large reward for their safe return.
Howard has stolen the gyrostabilizer from the ruins and is taking it to the three escapees to bargain it exchange for their rescue, with the added incentive of the reward they would get for the children's safe return. The escapees tell Howard they can only take one person with them, so Howard decides to accept the offer, and send help for the others later. Once the escapees have the gyrostabilizer, however, they turn on Howard and are about to kill him, until they realize that Howard took the wrong component.
Menori, acting as spokesperson, tells the escapees to put down their weapons and move away from them, and Brindo plays along. They start the hostage exchange, but Brindo catches Kaoru heading towards the discarded weapons, and Zilba pulls out a needle gun and shoots at him. In the resulting confrontation, Howard gets hit by a needle. The children cross the river to escape, but find themselves still in range of Brindo's laser gun. Things look dire until Adam arrives, followed by the giant crustacean from the ruins, acting under Adam's unconscious control, which distracts the escapees long enough for the children to escape. They head for the ruins, relying on the illusory forest to slow the escapees down, leaving Kaoru behind to watch them.
The escapees are becoming increasingly frustrated by the illusory forest, while Porte, Chako and Shingo make some progress in interfacing the gravity control unit with the alien equipment. The children get excited, but Kaoru returns with sobering news - the escapees are starting to figure out the forest. Since Porte needs two or three more days, Kaoru, Bell, Luna and Menori plan traps to slow them down. Adam, looking dejected, sneaks out and finds Pague in the illusory forest outside. He confides in Pague that despite Luna's offer to take him back to their colony with them, he doesn't really want to go - this planet is his home.
The children put their plans into action, first separating the escapees, then trapping Bob in a cage and catching Brindo in a snare. However, Kaoru is tied down fighting Zilba. Brindo quickly frees himself, and soon corners Luna, Bell and Menori, but Kaoru shoots the gun out of his hand with an arrow, and Bell smashes it with a rock. Bob also breaks free, and the three regroup and close in on the children. Suddenly, the herd of pagues - with Pague himself in their midst - stampedes between the two groups, allowing the children time to escape. When the herd moves on, Bob tries to follow the children, and falls into a pit trap.
Knowing they can't sacrifice Pague for their own benefit, the children decide to give up on fixing the ruins and steal the Orion instead. They hide in the control room and close up the floor, then open up the outer door. They lure the escapees into the inner chamber with the terraforming device, then lock them inside, open the floor once again and escape, taking the gyrostabilizer with them and closing the door behind them. They head for the beach, but behind them, Bob batters down the inner door, and Brindo uses a miniature bomb on the outer door.
On the Orion, Kaoru familiarizes himself with the controls, Porte, Shingo and Chako head for the engineering room, while Sharla and Adam hide in the aft cargo hold. On the beach, Bob makes a raft from logs, and as the children race to intercept, they cast off. Using Bob's cyborg arm as an outboard motor, they quickly move out of arrow rage. Luna uses her power to warn Adam, and he warns the others. Porte installs the gyrostabilizer and the engine powers up. However, as Kaoru begins liftoff, the escapees board the ship through the aft cargo hold's hatch. They pass Sharla and Adam without noticing them, and head for the bridge, where the rest have holed themselves up.
The children find Porte hanging from a tree and bind his wounds, then head for the ruins. There, they find that both the Orion and the ruins have been all but destroyed. The children are all stunned, but Adam is especially distraught, as the ruins represented his only link to his parents. Luna suggests heading to the mainland to find the main terraforming machine, as they may also find another spaceship there, but the others, still reeling from the shock, decide it would be better to rebuild the basis of their lifestyle first, and consider bigger things afterwards.
With Shingo designing and Porte giving technical advice while recuperating from his injuries, the children start to build their ship with Pague's help, using the largely intact hull of the Orion for the main body, and searching the forest and ruins for parts and components. However, a disagreement caused by lack of parts is starting to open a rift between Shingo and Porte. Since the gravity control unit they found wouldn't be powerful enough to produce both lift and propulsion for their ship, Shingo comes up with the idea of using sail power for propulsion, but Porte rejects it outright, not willing to ignore centuries of tradition in spaceship construction.
As the children finish construction on the ship and load supplies for the journey, Porte visits each one except Shingo and gives them words of advice and encouragement. The children turn to Sharla to give the ship a name, but she asks for time to think on it. That night, they head back to Everyone's House for their last night on the island. As Menori plays her violin, they think over the many things that have happened to them. Later, after everyone has gone to bed, Shingo finds Porte sitting by the fire. Porte gives Shingo his mechanic's jacket, and the two lie side-by-side.
A few days into the trip, first Shingo and Adam, then Menori, Sharla and Howard become incredibly seasick. In addition, the ship has become becalmed, causing some concerns over provisions. Howard and Menori try to talk Luna into turning back to the island they came from, but Luna stands by her original decision. Luna stands watch in the crow's nest, brooding over things and zoning out to the extent that she fails to notice a huge storm brewing right behind her, even when it is right on top of them.
Bell tries to jump in after Luna, but the others hold him back. Kaoru attempts to turn the ship around, but because of the measures taken to avoid capsizing during the storm, the steering won't work. As Luna drifts out of sight, Shingo blames himself for not anticipating such a storm, but Chako is confident in Luna's ability to survive. In the ocean, Luna is being buffeted around by the waves, kept afloat only by her lifejacket and her memory of her father.
Heading for the continent once more, the children have realized that something happened to Luna on the island. Chako scans Luna and discovers nanomachines in her bloodstream, which were the reason for her quick healing. She scans the rest of the children as well, but only Adam has them too, which explains why Luna and Adam are able to communicate, why Luna could hear the mysterious voice, and why she could open the door to the ruins. Luna is extremely concerned that she has nanomachines, but tries to behave as normal in front of the other children. However, they can tell that it's just an act, and after three days, they plan a cheer-up-Luna surprise party.
Kaoru pilots the Orion up a river to find a place where they can come to shore, and they decide to stop for lunch on solid ground. As the children set up a picnic, they all notice that Sharla has become a much stronger person than she used to be, and conversation quickly turns to everyone's parents. Luna, however, as the only one of the human children who is an orphan, becomes saddened by the conversation, and Bell notices. As the children plan their route, they decide to spend the day replenishing their supplies. Suddenly, an earthquake occurs.
On the Orion, Chako determines that virus-like nanomachines have entered Adam's body and changed the nanomachines already there into malignant ones, and they probably entered through the scrape on his hand. They decide to head directly for the nearest sub-terraforming machine. After passing through a forest, they reach an ancient, crumbling city. They stop by a large building that they hope is a hospital, but the medicines they find had already decomposed long ago. Chako estimates them to be five hundred to a thousand years old, the same age as Adam's ruins. When Howard finds writing on a medicine bottle that's the same as writing they saw in the ruins, they realize that Adam's people had come from this planet, which raises the question of why he was in a spaceship on the island.
The children enter the terraforming machine, leaving Sharla behind to look after Adam. Inside, Luna finds a stairway leading deeper, where they are attacked by a large humanoid robot, which Chako identifies as a maintenance robot. They defeat it when Kaoru plunges his knife into its head. The strange voice which Luna heard earlier speaks to Luna through the robot. It identifies itself as the main computer that manages the terraforming machines, Survive. With Luna translating for the other children, Survive recounts the history of the planet.
The Orion travels through a desert, but progress is slow, as sand keeps getting into the engine room, forcing them to stop while Shingo and Chako clean it. When they're on the move again, they have lunch together, but food and water supplies are starting to get low. To cheer them up, Sharla shows everyone a desert flower that she found, made of crystallized sand, but Howard, getting frustrated and afraid, grabs it and smashes it on the floor. Adam realizes that Sharla has been sharing her water ration amongst everyone else, and tells Luna, but Sharla promises Luna that she's ok.
The children sit stunned by the side of the quicksand pit. Luna and Shingo each blame themselves - Luna for suggesting they go to the mainland, and Shingo because the Orion was his design. Menori, knowing that they would never survive in the desert in the day, forces them all to start walking. They walk by night and rest by day, reaching a forest at the edge of the desert the following night. Chako tries to lighten the mood, but Shingo becomes angry at Menori's hard-line stance and the two get into an argument. As they lie down to sleep, they all recall memories of Howard and Sharla.
The children find a door in the hull, which opens when Luna holds up her hand. Inside, they encounter a maze of passageways, but drones quickly find them and they are forced to flee. After they run past one section of corridor, a small being emerges from a hatch in the wall, and instantly recognizes Adam. The small being, who speaks a language only Luna and Adam can understand, asks the children to follow him, but assuming him to be another enemy, they run from him. When the drones chase the being instead of them, they realize they can probably trust him, and when he appears in front of them from another hatch, they decide to follow him.
Outside, the children gather food while avoiding the drones. They discuss how much the area reminds them of their island, and Adam is excited to see a pague, except it's quite small. As the pague returns to its mother, two drones arrive, but someone shoots arrows at them from the bushes and destroys them. In a moment, Howard and Sharla emerge from the bushes. The children have a tearful reunion. Sharla tells the others that when they were sucked down by the quicksand, they fell into flowing water underground. Howard, however, sits in stoic silence. Sharla passes it off as him being tired, and prevents Chako from scanning him. When Luna and Sharla make skin-to-skin contact, Luna feels a weird sensation.
Outside in the forest, Sharla stands communicating with a drone, agreeing to continue observing Luna. Elsewhere, Luna senses the drone, but when she and Kaoru run there, they only find Sharla. Worried, they head back to the hidden room. Together, they come up with a plan to reach Survive's chamber and accost the computer directly. The security drones act largely autonomously, guided by the sensors in each section - Shingo and Chako will use a modified chip to disable the sensors, meaning that so long as they stay out of direct sight of the drones, they won't be able to detect the children. Luna and Kaoru go with them for defense.
Chako reveals to the others what they suspected, that Howard and Sharla were being controlled by Survive. Luna and Kaoru follow Howard and Sharla, but encounter drones trying to force their way into the hidden room. They return to regroup, but realizing there are no more safe places to hide, they decide to attempt a frontal assault on Survive's room. Shingo finds two infrared inhibitor particle nebulizers which they can use to confuse the drone's sensors in the same way that Howard's mirror worked earlier. In Survive's room, Survive tells Howard and Sharla that he needs to obtain Luna's power for himself.
Survive shows the children images of earthquakes causing damage all over the continent, but he cannot determine the cause of them. He explains that he needs Luna's power to save the planet, even if he has to absorb her to get it. The children discuss escaping the planet, but Survive threatens them with a huge swarm of drones. Luna offers to investigate the cause of the imminent destruction in exchange for their safety - though Survive is supremely logical and has access to all the data, the humans have the ability to see connections and make intuitive deductions.
Survive has detected the gravity storm approaching, on a direct collision course with the planet, due to arrive in three days. Shingo thinks they can save the planet by using the gravity control unit on Survive's spaceship to create an inverse gravity field, cancelling out the gravity storm. With Survive's computing power, the children test a simulation using the anti-gravity sled's smaller unit, and are successful. However, since the plan requires detaching the gravity control unit from Survive's ship and sending it into the storm, Howard and Menori object, saying they should use the ship to return home while they can - there are no other spaceships or sufficiently powerful gravity control units on the planet. The other children agree that they have to save the planet, and Howard storms off.
The children spend time preparing for departure - learning how to fly the ship, testing systems, ensuring everything is ready. On their last night before they start the mission, the children all gather in the forest by the lake, and remember the events that brought them to this point. Howard worries that it might be their last night, but Kaoru tells him they're not going so they can die - it's so they can live. The next day, they evacuate all of the coffins from the ship, leaving Adam and Tako behind to take care of them and the planet, and then prepare for takeoff. With Kaoru as pilot and commander, Shingo on engineering, Chako looking after the computer, Bell on power systems, Menori and Luna on flight plan and navigation, Howard on life support, and Sharla on communications, the takeoff happens without a hitch.
Shingo realizes that it is no longer possible to detach the gravity control unit from the ship - to stop the storm, they'll have to take the whole ship into the storm. Kaoru and Bell each volunteer to do it alone while the others escape, but the rest remind them they agreed to do it together. However, Luna, still with Survive, activates their seatbelts and ejects the entire bridge from the ship. She farewells each of them individually, then takes the ship into the gravity storm.