Our main protagonist is a girl named Spensa. The book begins with Spensa as a young girl who is finally getting to go above ground with her father for the first time in her life. Spensa and her family live in underground caverns due to the space debris that is constantly falling to the planet's surface (the planet is called Detritus) and due to trying to avoid the aliens who always attack them called the Krell. Her father is a fighter pilot for the DDF (the organization that is comparable to our Air Force) and is one of the most well known pilots due to his prowess fighting against the Krell.
There are several groups of people who live on Detritus. When their ancestors crashed aboard the ship called Defiant, the survivors found their way to the underground cave system where they were able to survive due to the previously installed tech which was left abandoned after the last people of Detritus. No one knows much about the previous inhabitants since that information has been lost, they just know they were human rather than alien. After many years, the separate groups begin helping each other again and come together as one people. Although they do still live in separate places they aren't segregated anymore and are all just known as Defiants.
While Spensa and her father (callsign: Chaser) are on their way to the surface a call comes in to her father's radio saying that he is needed because a huge amount of Krell ships are inbound. Chaser tells Spensa to go back home and he takes off. Spensa gets lost on the way back so by the time she makes it back to their underground home the battle is over and she finds out that her father abandoned his flightmates in the middle of the mission and was shot down by his squad due to turning coward.
The book fast forwards 9 and a half years. Spensa is now a teen who is constantly looked down upon due to her father being labeled as not just a coward but THE coward. His name even comes up in conversations as a tool to keep kids in line, things such as "you better study hard, you don't want to be a Chaser". Spensa has lived in this shadow since her father abandoned his fleet and her goal in life is to become a pilot for the DDF, not just because she loves flying but to also prove herself to everyone who looks down on her.
She is about to graduate and is going to take the exam to see if she can become a pilot. She has studied all the ins and outs of flying for as long as she can remember and figures she is a shoo-in to pass the test. One of her classmates plants doubts in her mind though, saying that the DDF will never allow a coward's daughter to fly for them since it would make them look bad. Spensa asks her teacher if this is true since the girl that tells her this is the teachers daughter and although she doesn't outright say it, her body language and the way she dances around the question makes Spensa realize the girl was telling the truth.
She storms off to go hunting in the caverns (she hunts rats for her mother to sell in the local market with her homemade speargun) to cool down and then goes to the surface. While above ground a space debris shower hits and Spensa has to run for cover. She dives into another cave, farther out than shes ever been before, and finds a broken down spacefighter ship (a new kind, unlike anything the DDF has) along with a new type of slug creature that mimics her when she speaks (as closely as it can anyway, right now it just makes squeaking noises but eventually the more time it spends with Spensa as her pet the more it can mimic her and Spensa names it Doomslug. Doomslug can also teleport between places).
Spensa decides to go take the exam just in case there's a chance she could get in to flight school and arrives just in time to start the test. She realizes the test giver is none other than the head of the DDF, admiral Judy "Ironsides" Evans. Spensa begins the test but finds none of the usual test questions about ships and how they function but rather questions on all the classes the teachers knew she had skipped such as algae growing and cleaning. She realizes at this point that there's no hope of her getting into flight school because they've given her a special test that they know she'll fail. Dismayed, she sees several students turning in their tests almost as soon as they are handed out to them and it's revealed that this is because they don't have to take the tests since they are automatically allowed in flight school since they are sons and daughters of the "first citizens", which are the pilots who fought in the huge battle that Spensa's father was a part of (and consequently abandoned). The battle was historic and is treated with reverence because the DDF won against overwhelming odds and it is now called the Battle of Alta.
Spensa has one last trick up her sleeve and tries to go to Ironsides after the end of the test to give the woman her fathers pin and say that she is the daughter of a first citizen, even if her father did desert the battle. Ironsides denies her and tells her that she will never fly. Defeated, Spensa sits in the classroom for hours after the test. She picks up one of the first citizen students unfinished test and begins filling in the answers to all the questions. This person's test actually had questions about flying since theirs wasn't rigged. She then hears someone come in the classroom. She thinks it is the janitor and he's going to tell her to leave but it's actually Mongrel, another pilot who was her father's wingmate and also a first citizen. He picks up the test she's filling out and looks it over, seeing that she got almost all the answers right. He then places a cadets pin on the desk on top of the test and tells her to show up to flight school day after tomorrow and use the pin to get in. When she questions him on this he tells her that as a first citizen he holds more sway than the admiral and she won't be denied entry to the school.
She shows up for class and sees that Rig is also there. She wasn't sure if he had passed the test or not because he was pulled into the commanding office after the test so she thought he was in trouble for some reason but it turns out he was congratulated because he got a perfect score on the exam.
There are several other students in Spensa's class:
1. Jorgen (known as Jerkface, he is their flightleader)
2. FM (a girl who Rig has a crush on)
3. Hurl (Spensa's wingmate)
4. Quirk (real name Kimmalyn, she's a sweet girl who doesn't curse and is nice to everyone, she's Spensa's first friend at the school)
5. Morningtide (a girl who Spensa finds out doesn't speak much English so she begins helping her whenever Morningtide gets confused on their instructions)
6. Bim (a boy with blue hair, Spensa has a crush on him and it's revealed that he probably likes her too because there is a scene where he flirts with her)
7. Arturo (Jorgen's friend)
8. Nedd (Jorgen's friend, they went to school together before flight school)
9. Rig
Spensa also sees that Mongrel (real name Captain Cobb) is their instructor and they begin class. Rather than flying real ships they are trained on holographic machines to simulate flying. Spensa realizes quickly that although she knows how to fly it is much harder than it seems and she's not automatically great at it like she thought she'd be.
After class Spensa is pulled aside by Cobb and he tells her that Ironsides has commanded she not be allowed to stay at the dorm with the other cadets or eat in their mess hall. She knows it is because Ironsides wants her to give up but Spensa refuses to quit so she begins hiking to the cave she discovered every day and sleeping inside of M-bot, the ship she found in the cave. Doomslug keeps her company.
Over the course of their training, Cobb teaches them about the three types of weapons their ships have; destructors which are like regular guns but are not very accurate, light lances which are used to help maneuver tight turns during battle, and Inverted Magellan Pulse (IMP) which allow them to take down the Krell's shields (this tactic has to be done very close to the other ship and it knocks down the cadet's shields too so it has to be done in tandem with their wingmate firing on the Krell ship to take it out).
One day, Spensa comes to class and she realizes her helmet feels funny so she pulls it off and there are nodes inside of it. When she questions Cobb about it he tells her that Ironsides ordered it because they think her dad's cowardice (they later start calling it the Defect) is hereditary and they are trying to prove it.
While spending time in the cave Spensa begins trying to fix M-bot. She needs a new power matrix to get it going so she steals the one from Jerkface's car when he makes her mad one day by revealing to everyone that she is Chaser's daughter. She had been making friends with the cadets up to this point, especially Hurl, but now Hurl ignores her.
Spensa installs the power matrix and M-bot powers up and begins talking to her. He is a very funny AI who tells her that his memory banks have been corrupted and all he remembers is the last thing his pilot said to him: "Lie Low M-bot. Take stock, don't get into any fights, and wait for me here". He tells Spensa that his purpose must be to gather mushrooms since he has an extensive knowledge base of them and this is probably what his pilot meant by take stock. Spensa knows this isn't the case but she lets it go. M-bot also tells her she can't fix him to fight since his pilot's orders were to not get in any fights. She tells him okay but of course is planning to fix him up for fighting.
She realizes she's going to need help fixing M-bot so she asks Rig to help her. He tells her that since he left flight school (he dropped out after their first big battle, telling Spensa flying was always her dream and he had just been along for the ride but he knows he's not good enough to do it now) he was offered a position in the engineering department which will allow him to get parts to fix M-bot.
One day while they are in the cave working on M-bot he tells her that his sensors have registered a bunch of ships heading toward the planet. Spensa realizes it must be a Krell attack and hurries back to base in case the cadets are called in to assist in the fight.
When she arrives her ship is the only one outside the hangar so she takes off quickly to catch up to her squad. Jorgen tells her they are having a hard time and to help Morningtide, who has three Krell ships tailing her. Spensa tries her best but Morningtide is shot down.
After an extensive battle Cobb orders them to hold back until further orders. A Krell lifebuster shows up (it's like a huge blimp that is a bomb, slow moving but deadly) and Bim says he thinks he can shoot it down. He goes after the lifebuster, asking Spensa to help him. Cobb tells Bim the lifebuster looks larger than normal and to hold back but Bim ignores him. Suddenly other ships come out of the sides of the lifebuster and Bim is shot down. This is the first time the DDF sees this tactic with the lifebusters but it's a tactic the Krell employ from now on in the fights. The Krell retreat since the DDF is attacking their lifebuster (the DDF thinks the lifebusters must be hard to produce since the Krell always retreat rather than risking them being destroyed during a fight) and Skyward Flight (the name of Spensa's squad) return to base, devastated at Bim and Morningtide's deaths.
During another battle, a huge chunk of space debris is falling to the planet's surface and several Krell are shooting at it. They are trying to destroy it because the wreckage will have a lot of acclivity rings in it which is what the DDF uses to make their ships fly, so the Krell want to prevent them from getting them and making more ships. Nedd sees two pilots from another squad being chased by the Krell and goes after them. Spensa follows to try to help them. The pilots fly into the space debris to try to get away. Nedd and Spensa follow but are unable to catch the Krell tailing the pilots. Spensa begs Nedd to leave because the debris will hit the planet at any moment and then they'll all be dead. He refuses so she uses her light lance to grab him, forcing him to stop and flee with her. He angrily tells her she really is a coward and she finds out later that he was so intent on trying to save those two pilots because they were his two brothers who were in another squad.
Later on, Spensa sees Cobb in the training room watching the holograms of the battle. He congratulates her on how well she fought. She asks him why he no longer fights and he tells her it's because of old wounds. She's seen his limp but tells him a bum leg shouldn't affect his flying and he tells her it's not his leg, it's the trauma of having to shoot down one of his comrades. Spensa realizes he's telling her that he's the one who shot down her dad when he turned coward.
Skyward Flight gets into another battle with the Krell a few days later. Hurl gets into a predicament where several Krell are chasing her and Kimmalyn tried to shoot them but misses. Hurl's ship starts to go down and Spensa begs her to eject but Hurl claims she might be able to land it and that she isn't a coward (early on it is said that if a cadet ejects during training they aren't allowed to proceed with their training because it shows cowardice since they are more worried about saving themselves than trying to save the expensive ships and land them). Her ship goes up in flames and they know she's dead. Kimmalyn blames herself for Hurl's death since she was unable to shoot the fighters tailing her. She later drops out of the flight school due to her grief. Arturo is also pulled from the school by his family due to the dangers after his ship is almost shot down in the battle too.
The cadets are given a week off to cope with the loss and Spensa tells the others she's going to go out to Hurl's ship to give her a proper funeral since Cobb told them it will probably be a week before the DDF can retrieve her. Jorgen catches up to her on her way out there and offers to take her in his car. They find Hurl's crashed ship and Spensa cautiously goes up to the pilot seat. She's hoping to see that Hurl managed to escape but those hopes are gone when Spensa sees that she is in there dead. Jorgen and Spensa give her a funeral by burning her body in the ship. Jorgen opens up to Spensa and tells her that he loves flying and that he wants to be a pilot but that he's only in flight school for probably about six months, just long enough to gain a good reputation and then his family will be pulling him out to go into politics. He doesn't want to do it but feels he has no choice and can't disobey his family's wishes. Spensa gets angry, not at him but at the fact that the rich can do that while the poor are forced to fight all their battles for them. They don't want to risk their children but are fine with risking the lives of all the lower class citizens by making them fight.
As they start to leave, Spensa sees that although Hurl's ship was broken apart the last part she needs to fix M-bot is there and in one piece. She asks Jorgen if he will help her get it. He questions her on what she needs it for but she says she can't tell him. He figures it out though since he knew she must have been the one to steal his power matrix from his car but he thinks she's building her own ship, not that she found one and is fixing it.
When they get back to base Spensa goes to Cobb to give him Hurl's cadet pin to give to her family. She asks Cobb if she can watch some of the old battle holos since they are off for a week and she wants to keep herself occupied. She is surprised when he immediately agrees and hands over his key to the locked room with all the videos in them. She realizes he wanted her to ask, knowing that she's wanting to find the holo of the battle of alta and watch it to see what really happened with her father. Cobb tells her that cadets aren't allowed in the archives and to say that she's getting something for him with his permission if anyone sees her. She goes to the room and finds the holo, steals it and heads to M-bot to play it in his cockpit where she won't be seen by anyone else.
When she watches the battle, she sees her father fighting and then flying up into a hole in the space debris around the planet like he is trying to find where the Krell are coming from through the gap that appeared. She is elated to see that he wasn't a deserter as everyone said and was instead trying to help his squad, but then the holo continues and it shows him flying back down through the gap and attacking all his team. She asks M-bot to play the audio and hears the conversations of the pilots. Her dad asks Ironsides (who was the flightleader of their squad) if he can have permission to go through the gap that appeared and that he feels he needs to because he can hear the stars. Curious as to what is up there too she agrees. They lose communication when he goes through the space debris belt and then when he comes back down the only audio is him saying he will kill all of them. Spensa asks M-bot if this could be faked and he tells her no, that it is authentic. She wonders why the DDF would just label her father a coward when the truth is so much worse and he's actually a traitor.
A few days later Spensa goes to the cave to find that Rig has fully repaired M-bot now so Spensa takes him flying. He still has a simulation of the battle of alta in his files and asks her if she would like him to play it for practice since although his directive tells him not to fight that fighting fake ships should be okay. She agrees and begins the simulation with him. They go higher in the sky than she's ever been before, almost to the debris belt, and she begins to hear the stars just like her father. She gets scared and screams at M-bot to stop the simulation, now wondering if everyone is right and the defect is affecting her too. M-bot tells her after their flight that he is going to shut down because he knows that Spensa will want him to fight and the only way he can avoid that and obey his orders is to shut down. She tries to talk him out of it but he won't listen and shuts down.
Spensa goes to see her family and talk to her grandmother to try to make sense of what happened to her dad. Her grandmother (who she calls gran-gran) tells her that when the Defiant crashed it wasn't just a tech failure but because Spensa's great grandmother was part of the crew and she had special abilities. She was able to cause the ship to leap through space/time with her abilities (which is called cytonic hyperdrive, M-bot always said his hyperdrive is offline but Spensa never knew what that was til now). When the Krell began attacking them and ordering them to surrender, rather than do so Spensa's great grandmother used her abilities to activate the hyperdrive and they wound up at Detritus below the space debris belt. The distance was so far that her great grandmother died after the warp and so they were stranded on Detritus since there were no other Deviations (what they used to call the people with this special ability) aboard the ship. The others began saying great grandmother was a traitor since she had now put them exactly where the Krell could get to them but that wasn't her intention at all, it was just to get them to safety. Since then, everyone has been afraid of the defect and it is seen as a bad thing that can cause the Krell to be able to control them rather than something that could save them all.
A while later during training Skyward Flight (what's left of them since it is now only Jerkface, Spensa, and FM) is combined with another flight group for maneuvers and while flying they see some Krell. The Krell spot them too and come after them. They hold them off but when a lifebuster is spotted the other more experienced flight crew is sent to deal with it. One of the pilots loses his wingmate and Krell are after him so Skyward Flight goes to save him. Spensa's ship is shot down and she ejects even though she knows this means she won't graduate. Rather than follow through and be a "hero" by trying to save her ship she remembers Cobb's training and ejects instead. She is right though and Ironsides kicks her out of flight school.
Everything switches to Ironsides point of view and a meeting she is having with the DDF. They are questioning her methods because they know they are losing more ships and pilots every day and soon the Krell will have them outnumbered. She tells them that she has a plan; another huge chunk of debris, a shipyard, that will contain enough acclivity rings to build hundreds of ships has been found coming toward Detritus. If they fight the Krell off rather than letting them destroy it they can turn the tide of the war. The rest of the DDF know that this will take every pilot they have in order to win and it will be as big as the battle of Alta but they don't see another choice and agree.
Spensa meets Nedd, Arturo, and Kimmalyn at their favorite restaurant to listen to the battle on Arturo's radio since it picks up the DDF voice channel. The battle seems to be going well but then it is revealed that a lifebuster has been spotted and is heading for the artillery cannons. The pilots manage to take it out but lose a lot of their force.
Arturo says that his family has a few ships underground that aren't part of the battle and are just for getaway purposes so he, Nedd, and Kimmalyn go to retrieve those to help in the fight. Spensa thinks of going to M-bot but since he's shut down doesn't know if it will be any use. Then another group of Krell is seen on radar coming in from the opposite side of the planet along with another lifebuster. The cadets, pilots, and DDF realizes the shipwreck and the large battle was just a distraction so that the Krell could finally catch them off guard. They know they aren't going to reach the lifebuster before it gets within blasting range and that it will take out the cities on Detritus. Spensa then remembers that Arturo's ship which was damaged is still in the hanger at the cadet base so she takes it to head for the lifebuster since she's the only one who will be close enough to try to reach it.
She begins battling the Krell ships and in the intensity she hears and knows the Krell's maneuvers before they are going to do them so she manages to stay alive. She doesn't understand how she knows what they are going to do, and while it's happening one of the DDF members asks Ironsides if she's ever seen anything like that before and she says "yes, once" referring to Spensa's dad. Spensa eventually gets hit and realizes it's from the black ships that are surrounding the lifebuster (one of the new tactic ships we discussed previously) and that she can't anticipate those ship's moves. Her ship goes down and she manages to land it safely but the Krell ships come after her wreckage to make sure she's dead. Right as they are about to fire on her a ship floats over her to block her and it is Mongrel flying M-bot.
Surprised not only that M-bot is awake again but that Mongrel is actually flying, she jumps inside the cockpit and Mongrel hops out and tells her she has to drive the Krell and bomber back into the sky because he hasn't had his afternoon coffee yet. Spensa tells him she thought she could hear the Krell in her mind and he tells her to fly anyway, that he knows she won't turn on them and that she's got nothing to lose at this point.
When Spensa gets in M-bot, he tells her that he called Cobb because when he turned himself off he didn't fully shut down and he's just been thinking this whole time and he wrote himself a new program that replaced his previous command and his new one is that he must follow the commands of his pilot, and he has chosen a new pilot (her).
She flies up to fight the Krell and Arturo, Kimmalyn, and Nedd arrive to help. They tell her that Jorgen and his crew are about 2 minutes away. They all work to take out the Krell but the lifebuster is getting closer and closer to being able to detonate. Spensa is still hearing the Krell in her mind and she hears them say there is a countdown of 100 seconds until detonation begins. Desperately, Spensa uses her light lance to sever the clamps on the bomb. She then dives after the bomb and uses her lance to clamp onto it and use it's momentum to swing herself around to give her enough force to pull the bomb back up. She then shoots toward the space debris belt pulling the bomb behind her and away from Detritus. She knows she's going to die when the bomb explodes but she accepts it to save everyone else. M-bot suddenly says that his cytonic hyperdrive is online and they vanish as the bomb explodes. In the nothingness Spensa says that she sees a field of white, a billion stars, like eyes opening at once shining on her.
She is thrown back in her seat and back into her body and M-bot tells her they are now 100km from where the bomb detonated. He says there's no discrepency in time but they have traveled that far instantaneously. Spensa is happy they are safe but says that the 'somethings' that were in the nothingness knew what she had done and didn't like it.
Spensa looks up and sees a hole, the debris shifting just right to make an opening exactly like the day it happened to her father. She begins to hear the stars and tells Ironsides on her comm that she's going in and that if she comes back crazy like her dad that M-bot doesn't have destructors so they'll be able to shoot her down. Ironsides begs her not to go but she ignores her.
When she goes into the debris field she realizes that it isn't just debris but huge platforms that could hold the entire city of Alta with thousands of unlit buildings on them, and she sees that people used to live on these platforms.
M-bot draws her attention to the end of the tunnel they are going through in the debris field and says that one of the lights out there isn't a star. As they get closer Spensa sees it is a space station and several ships are flying around it. The voice of the stars seems closer and Spensa realizes it is the way the Krell communicate to one another, in the nothingness between the stars. She wonders aloud "don't they know it's dangerous, that something LIVES in the nowhere, don't they know about the eyes?" M-bot tells her he doesn't understand what she means, that they are using sublight communication and superluminal ones. Spensa sees that the ships aren't fighters, more like cargo ships so she doesn't immediately attack. Something hits her then like a physical force and she feels it trying to crawl inside her mind and override what she's seeing. M-bot puts up his stealth shield and jammers to help her and she comes back to herself.
The voices vanish and the pain eases off and Spensa tells M-bot that she knows now the Krell made her father see what they wanted him too and that they made him think his friends were dead and that he was attacking the Krell when he went back through the belt. She says that the defect must allow her to see into the nothingness but also makes her vulnerable to the mind control of the Krell.
As they get closer to the ships (they are now invisible to thanks to M-bots cloaking) Spensa sees that the things inside the ships look like the photos of Krell armor she's seen (no one has ever seen a real Krell, all they've ever recovered from wreckage is the armor) but that the armor is different colors from the fighter's armors that they normally fight. The sides of the ships are engraved with words in a strange language and M-bot is able to translate them. They say "Penitentiary Maintenance and Containment of Earthlings".
Spensa tells M-bot to ease up on his jamming so she can hear what they are saying and the aliens/Krell start freaking out saying that she's looking at them and that she must want to eat them. One of the other creatures says she can't be looking at them because they are overwriting her vision (they don't know M-bot is jamming them). That creature tells the one freaking out to tow in the ship since it isn't a standard DDF model so they can study it. When it gets close Spensa bares her teeth at it and it screams and flies away, saying that she's too dangerous and this should be a job for fighters. M-bot starts hacking into their programming to try to get more info on them and fighters come to attack them so they have to fly back through the hole in the debris belt before he can get very much info but he tells her that he did get some answers for her.
The book ends with Spensa meeting with Ironsides, Cobb, and the other DDF along with Jorgen and Rig and explaining to them what M-bot found out: Detritus is a prison for humans, or to put it more politely, a preserve for humanity. There was an intergalactic war many years ago that was a case of humans vs. aliens (as in all the alien races, not just the Krell). When the humans were defeated a coalition was formed between the other alien races and they decided humans were too violent and unstable to be part of the intergalactic community. They demanded all human fleets surrender. When they came upon the Defiant and ordered its surrender the captain was going to but Spensa's great grandmother and many others on the ship felt they were innocent in this war and that's when she teleported them to Detritus. The group from the coalition who had been sent to get their surrender are the ones the humans now know as the Krell.
Since then, the coalition has been sending in the Krell to keep the defiants busy so that they do not have a chance to try to work out how to escape, but they are only allowed by the coalition to send so many ships at a time (up to 100) so as not to overwhelm the humans since the coalition wants to preserve humanity and not totally wipe it out to extinction. Spensa tells them that something has changed now though, because the last lifebuster that was sent WAS sent to wipe them out and since they defeated it the Krell are now scared.
Ironsides says that doesn't really change anything because the Krell are still the superior force and Spensa tells her the aliens guarding them aren't fighters but just prison guards who fly mostly unmanned drones to overwhelm them with numbers. Spensa also says they have an advantage because she can hear what they are thinking, and even though she doesn't say it she contemplates in her head about how she's also at an advantage because she can teleport....if she can just figure out how to do it again and control it.