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. On board were Julian "Bean" Delphiki and his three infant children – Andrew "Ender", Carlotta, and Cincinnatus – all of whom had Anton's Key turned. This genetic alteration, which Bean passed on to his children, granted them all extremely high intelligence, but caused their bodies to grow uncontrollably, which was likely to kill them by the age of 20. Subjectively, they had been flying near light-speed for five years, but relativistic effects mean that 421 years have passed on Earth. When the family left, scientists were actively trying to find a cure for their gigantism which would not diminish their intelligence. Several generations passed, and they were forgotten, their mother and "normal" siblings having died centuries ago. The three children had only been alive for six subjective years. Bean's life had been extended by the low gravity on board the Herodotus, which allowed his heart to keep beating despite his increasingly gigantic size. At 4.5 meters tall, Bean must remain in a lying position in the cargo bay so as not to over-exert himself. He controlled and watched everything on the ship through his holo-top terminal, often prompting the children to have secret meetings they believe the Giant (Bean) cold not hear.
In one of these meetings, the militarily-minded Cincinnatus (nicknamed "Sergeant") tried to enlist the aid of his siblings in killing their father, saying that he was a drain on resources. Carlotta was unwilling to take a stance, but Ender punched Sergeant and broke his nose for proposing such an idea, thus ending his brother's domination over the family. Ender and Carlotta told Bean about Sergeant's plans, and Bean put all three children in their place, reminding them they were each as intelligent as the other. Sergeant had been imagining threats to their security where there were none, because he believed the Giant meant to pass his soldier role onto him. Ender took on the bulk of the genetic studies by monitoring the advances made by the scientists on Earth. Carlotta served the family by taking care of every aspect of the spacecraft, since Bean was 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 could not be cured, Carlotta noticed an unknown spacecraft in geosynchronous orbit around an uncharted planet in the Goldilocks zone. Bean and his children deliberated courses of action. If they altered their course, they must slow down to turn, possibly killing Bean with the increased gravity. However, they could not anticipate who or what was in the spacecraft; it may attack them, or they may be detrimental to the survival and progression of the human race. This hypothesis was solidified when Sergeant deduced that the ship is a Formic Ark, a colony ship that had been in flight for close to a millennium.
Bean sent Sergeant alone to investigate the ship, and he escaped an attack by small Formic-like animals they called "rabs"(rat crabs). After this initial encounter, Bean revealed his full plan to his children. They must find out who was 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 commanded defenses as Carlotta led their group to the helm with Bean in contact the whole time. The spray proved effective, and they soon found the Hive Queen's chamber to find her, and many workers, dead. Eventually they found living male Formics, drones, in one of the piloting helms.
In an attempt to communicate, Ender surrendered himself by drifting close to them in zero gravity. The male drones came close and communicated with Ender via mental images. The group learned that the Ark was sent long before Ender Wiggin, whom Bean's son was named for, wiped out the Formics in the Third Formic War. After the Queen on their ship died, the workers died without her mental link, yet the males lived and tried to survive to keep the ship running despite losing numbers to the feral rabs, whose population had doubled after the Queen's death. The group struck a deal that if the children could wipe out the rabs, they could stay with the Formics and help cultivate the planet. When Bean learned from the male drones that Ender Wiggin was in possession of a Hive Queen cocoon, and that Formic workers did in fact have minds of their own contrary to the popular belief, he demanded to speak with the Formics in order to warn Ender, despite risking his life in the journey.
Accepting that his children had achieved beyond his wildest expectations, Bean risked 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 communed for three days with the Formic males. Though the Formics thought it was silly to believe the Queen would hide anything from them, Bean learned that workers could rebel against a Queen and regain their free will. After Bean slept for a while, his children woke him informing him that Ender had devised and administered a virus that would 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 looked at the beauty around him and remembered all those whom he loved and who loved him in his life. With his children's help, he stood for the first time in years, and walked with labored breathing in the sunlight. Happy for his children and for his own short but brilliant life, Bean lied down and died in peace.