At the end of Shadow of the Giant, Bean flees to the stars with three of his children--the three who share the engineered genes that gave him both hyper-intelligence and a short, cruel physical life. The time dilation granted by the speed of their travel gives Earth's scientists generations to seek a cure, to no avail. In time, they are forgotten--a fading ansible signal speaking of events lost to Earth's history. But the Delphikis are about to make a discovery that will let them save themselves, and perhaps all of humanity in days to come.
For there in space before them lies a derelict Formic colony ship. Aboard it, they will find both death and wonders--the life support that is failing on their own ship, room to grow, and labs in which to explore their own genetic anomaly and the mysterious disease that killed the ship's colony.
The starship Herodotus left Earth. Onboard were Julian "Bean" Delphiki and his three infant children – Andrew "Ender", Carlotta, and Cincinnatus – all of whom have Anton's Key turned. This genetic alteration, which Bean passed to his children, grants them all extremely high intelligence, but causes their bodies to grow uncontrollably, which is likely to kill them by the age of 20. Subjectively, they have been flying near light-speed for five years, but relativistic effects mean that 421 years have passed on Earth – the year is now 2631. When the family left, scientists were actively trying to find a cure for their gigantism which would not diminish their intelligence. Several generations have passed, and they have been forgotten, their mother and "normal" siblings having died centuries ago. The children have only been alive for six subjective years. Bean's life has been extended by the low gravity on board the Herodotus, which allows his heart to keep beating despite his increasingly gigantic size. At 4.5 metres tall, Bean must remain in a lying position in the cargo bay so as not to over-exert himself. He controls and watches everything on the ship through his holo-top terminal, often prompting the children to have secret meetings they believe the Giant (Bean) cannot hear.
In one of these meetings, the militarily-minded Cincinnatus (nicknamed "Sergeant") tries to enlist the aid of his siblings in killing their father, saying he is a drain on resources. Carlotta (whose specialty is engineering) is unwilling to take a stance, but Ender (an expert biologist) punches Sergeant and breaks his nose for proposing such an idea, thus ending his brother's domination over the family. Ender and Carlotta tell Bean about Sergeant's plans, and Bean puts all three children in their place, reminding them they are each as intelligent as the other. Sergeant has been imagining threats to their security where there are none, because he believes the Giant means to pass his soldier role onto him. Ender takes on the bulk of the genetic studies by monitoring the advances made by the scientists on Earth. Carlotta, who feels slightly left behind with the genetic studies serves the family by taking care of every aspect of the spacecraft, since Bean is too large to work on any sort of repairs.
After despairing at the condition of their lives, and in the light of the discovery that their condition cannot be cured, Carlotta notices an unknown spacecraft in geosync orbit around an uncharted planet in the Goldilocks zone. Bean and his children deliberate courses of action. If they alter their course, they must slow down to turn, possibly killing Bean with the increased gravity. However, they cannot anticipate who or what is in the spacecraft; it may attack them, or they may be detrimental to the survival and progression of the human race. This hypothesis is solidified when Sergeant deduces that the ship is a Formic Ark, a colony ship that has been in flight for centuries.
Bean sends Sergeant alone to investigate the ship, and he escapes an attack by small Formic-like animals they call "rabs"(rat crabs). After this initial encounter, Bean reveals his full plan to his children. They must find out who is piloting this ship and take their resources in order to terraform the planet. It was Bean's intention all along to have his children live on this planet and found their new species in safety as soon as he picked it up on radar as lying within the Goldilocks zone. Armed with Sergeant's weapons and a sedative fog spray Ender devised, Sergeant commands defenses as Carlotta leads their group to the helm with Bean in contact the whole time. The spray proves effective, and they soon find the Hive Queen's chamber to find her, and many workers, dead. Eventually they find living male Formics, drones, in one of the piloting helms.
In an attempt to communicate, Ender surrenders himself by drifting close to them in zero gravity. The male drones come close and communicate with Ender via mental images. The group learns that the Ark was sent long before Ender Wiggin, whom Bean's son is named for, wiped out the Formics. After the Queen on their ship died, the workers died without her link, yet the males lived and tried to survive and keep the ship running despite losing numbers to the feral rabs, whose population had doubled after the Queen's death. The group strikes a deal that if the children can wipe out the rabs, they can stay with the Formics and help cultivate the planet. When Bean learns from the male drones that Ender Wiggin is in possession of a Hive Queen cocoon, and that Formic workers do have minds of their own contrary to popular belief, he demands to speak with the Formics in order to warn Ender, despite risking his life in the journey.
Accepting that his children have achieved beyond his wildest expectations, Bean risks his life by docking with the ark's cargo hold to float down into the ecotat. Lying in the grass and basking in the artificial sunlight, Bean communes for three days with the formic males. Though the Formics think it is silly to believe the Queen would hide anything from them, Bean learns that workers could rebel against a Queen and regain their free will. After Bean slept for a while, his children wake him informing him Ender devised and administered a virus that will develop an organelle to shut off their growth genome, leaving their intelligence intact but saving them from the giantism half of Anton's Key.
With renewed hope for the future, Bean looks at the beauty around him and remember all those whom he loved and who loved him in his life. With his children's help, he stands for the first time in years, and walks with belabored breathing in the sunlight. Happy for his children and for his own short but brilliant life, Bean lies down and dies in peace.