The day after 17-year-old Kady Grant breaks up with her boyfriend, Ezra Mason, BeiTEch Industries attacks their planet. BeiTech Industries is a corporation that wants the planet’s secret mining organization for its own.
BeiTech launches ordinance and chemical warfare on the planet’s inhabitants. Several thousand, including Kady, her mother and Ezra are evacuated to three waiting spaceships: Alexander, Hypatia and Copernicus. Hypatia and Copernicus are civilian transports and not capable of battle, leaving only the Alexander to stave off any attacks by BeiTech’s warship, Lincoln.
The three refugee ships have sent out distress calls, which have not been answered. They are limping their way through space to get to Heimdall, a jump station. The story is told through emails, transcripts, interviews, confidential reports and AIDAN, the artificial intelligence that runs all three of the ships’ computers.
The military, which is housed on the Alexander, conscript anyone on the three ships who have any kind of skill. They work to repair the damage aboard their ship. They also draft anyone of age and who has good reflexes to train as pilots. Ezra is conscripted to become a pilot and help defend the ships should the Lincoln make another attack. He is taken aboard the Alexander.
Kady’s temperament is such that they do not put her in the military. They do recognize her computer skills, so she is co-opted to help in that area. Kady is on the Hypatia. She begins to hack into the Hypatia’s computer to try and get a realistic idea of what happened and what their chances are of survival.
This gets her noticed by another computer geek known as CitB. He is in a position to teach her how to maneuver through the safeguards, and the two work together to find out what is happening on the ship. Ezra makes several attempts to get in touch with Kady through email from the Alexander, but she does not initially answer him.
Ezra is sent out to fly dogfight drills when AIDAN issues commands for the pilots to stop running drills and focus their weapons on the Copernicus. When Ezra’s Major tries to contact his general aboard the Alexander, AIDAN refuses to patch him through. As Ezra watches, multiple shuttles from the Copernicus explode and others take flight toward the Alexander. Then AIDAN arms the Alexander’s nuclear missiles and blows up the Copernicus.
AIDAN then demands that Ezra and his fellow pilots destroy the shuttles that have left the Copernicus and are trying to reach the Alexander. The pilots refuse, and the shuttles are allowed on board, but they are quarantined as AIDAN insists the crew is carrying a fatal disease. The military aboard the Alexander lie to the civilians and claim that the battleship Lincoln destroyed the Copernicus. They then shut off AIDAN as they attempt to discover why the computer system went haywire.
They have four weeks until they reach the jump station, and they will not be able to successfully navigate the jump without AIDAN online. They will also be helpless against the Lincoln should the battleship catch up with them. Kady and CitB soon realize that AIDAN is offline and try to find out what really happened.
Kady reaches out to Ezra when she sees his name come up on a court-martial list. He escapes punishment, but his superiors are executed for spreading the rumor that AIDAN destroyed Copernicus. Kady manages to hack the computers between their ships so she can begin to instant message Ezra in seven-minute intervals.
Although glad to hear from her, Ezra will not divulge any classified information. Through an official transcript, the reader learns that BeiTech had released a virus on the planet. Some on the Copernicus had it, and it was spreading. In an effort to keep the virus contained, AIDAN destroyed the ship. Kady’s mother, a scientist, had been sent to the Copernicus to find a cure for the disease. She was among the casualties.
Kady and Ezra reignite their romance over emails and instant messaging chats. CitB convinces her to use Ezra to plant a device in the Alexander’s computer so that they can hack into it and try to figure out what is going on. Ezra only agrees when a good friend is left behind in the holding bay after his squad went in to investigate the shuttles from the Copernicus. The rest of the squad is being debriefed, but his friend was forced to remain in quarantine.
Kady assures Ezra that all the computer virus will do is help her retrieve the information on his friend. Instead, Kady is able to retrieve all kinds of classified information, including the transmissions regarding the disease aboard the Copernicus. It affects the body’s nervous system, making people at first jumpy and nervous, as if they are suffering from PTSD. Later, they become paranoid and violent. The paranoia seems to revolve around the notion that people are staring at them, watching them. The inflicted go insane, killing those closest to them in an attempt to be free of the paranoia.
When the virus aboard the shuttles spreads, they began to revolt and kill each other. The troops were sent in to try and help any who were not already infected. What they saw was the evidence of vicious murders. A young girl cut Ezra’s friend’s bio-suit with a knife, thus risking infection. While the rest of the troops escape, his friend was forced to wait behind in the airlock to either get the disease or get killed by the infected when they broke through the doors.
The acting commander aboard the Hypatia begins to consider separating from the Alexander and making a run for the jump station on her own. The Lincoln is closing in on them; without AIDAN, they are sitting ducks. The Alexander conscripts CitB, now known as Byron Zhang, to help them bring AIDAN back online but also curbing its ability to control the ship’s functions.
Zhang and another computer expert are forced at gunpoint to transfer to the Alexander and continue working on AIDAN. Zhang comes up with the idea to send a virus to the Lincoln’s computer, but it will take time to develop the necessary computer code, which is something they do not have as the Lincoln continues to draw nearer.
As Ezra and the other pilots are sent to engage the Lincoln, the Alexander is forced to bring AIDAN online. The computer “wakes” slowly and assesses the incoming threat. As its “thoughts” become quicker, it begins to read the thoughts of the pilots and the computer experts. It realizes Zhang’s plan and finishes writing the code and transmits it to the Lincoln’s computer, temporarily disabling the ship and allowing the refugees more time to escape.
AIDAN realizes that the experts will try and turn it off again. It releases the infected people from the shuttles and leads them to Alexander’s bridge to kill the captain and other military officials. AIDAN seals off other areas of the ship in order to try and save the unaffected refugees.
Zhang manages to escape the bridge and finds his way to AIDAN’s control center. He begins to work to turn off the computer, but it will take days. After messaging with Ezra and Zhang, Kady decides to steal a shuttle and make her way to the Alexander. It is the only way she can help to disable the computer and maybe allow those she loves to escape before the infected are able to attack the rest of the refugees.
Some on the Alexander attempt to escape to the Hypatia. They are allowed to dock, but not leave the hanger for fear of contamination. One of the shuttles is purged; its occupants are left to float in space when they report that one of the crew exhibits possible symptoms of the virus.
Kady uses a portable device to stay in contact with Ezra. She must fight her way past the infected, even shooting one, in order to find him. He says he is hiding in the control room, but when Kady arrives, she finds Zhang, not Ezra. Zhang is destroying AIDAN, but when he sees Kady, he begins to attack her as he is infected with the virus.
In a moment of clarity, Zhang realizes what he is doing and intentionally electrocutes himself to save Kady’s life. As she mourns his death, AIDAN speaks to her and admits to having pretended to be Ezra to get Kady over to the Alexander, as she is the only one who can fix what Zhang destroyed.
AIDAN tells her that Ezra is dead. When Kady picks up an axe to wield against the computer, it tells her that the Lincoln has fixed its computer and will attack them within eight hours. The only way to save the rest of the refugees is by repairing the damage Zhang inflicted.
The number of infected continues to rise on the ship as well as the number of those they kill in their paranoid frenzy. Kady works furiously to fix AIDAN, even as the infected seek to find and kill her. She and AIDAN guide the uninfected refugees to the remaining shuttles so they can escape to the Hypatia. Although they lose hundreds along the way, they save even more.
The uninfected escape to the Hypatia and that ship flees from the approaching Lincoln battleship. Kady and AIDAN manage to evade the infected long enough to bring the Alexander’s nuclear weapons up and fire them at the Lincoln, but not before the BeiTech ship launches it missiles.
The Alexander is critically damaged, but AIDAN guides Kady to an escape pod. Although she is suffering from severe radiation poisoning, she hopes to leave the truth about BeiTech’s attack on her shuttle’s computer. After the destruction of the two ships, Hypatia returns and retrieves Kady’s shuttle. She is kept in quarantine for a week until they are sure she is not infected, and she is given medicine to reverse the effects of the radiation poisoning. Once it is determined she is not infected, she is allowed a visitor, Ezra. AIDAN only claimed he was dead so Kady would not be distracted from fixing the computer.
In a transcript of an intercepted computer conversation, the reader learns that Kady is now a member of Illuminae, an organization out to expose BeiTech. Kady reaches out to BeiTech’s leader, Leanne Frobisher, who happens to be Ezra’s mother. Leanne tries to get information as to her son’s whereabouts, but Kady reveals nothing. Instead, she promises to expose BeiTech’s attack and all its illegal activities. Leanne warns that Kady will never escape BeiTech’s reach and that she will die a painful death. The two adversaries end their conversation in a standoff with the prospect of future battles between them.