The novel explores the beginnings of the Forerunner-Flood War. It details Forerunner-Human contact with-in the "first dozen pages."
It is also revealed in the first chapter that Humanity once had a massive and sprawling prehistoric interstellar empire. This original empire ended some 10,000 years before the events of the book, when they went to war with the Forerunners and were utterly defeated. As punishment, the surviving Humans were devolved by the Forerunners and exiled back to their planet of origin, a world called "Erde-Tyrene" (known in the present as Earth) in the Sol system. The Human species was split into about half a dozen sub-species to reduce the chances of it once again allying and becoming strong.
The story opens on a Human steam boat on Earth, then called Erde-Tyrene. On board are two members of a human subspecies; one is a chamanune called Chakas, and the other is a hamanune (also called a florian) named Riser. With them is the young Forerunner Manipular Bornstellar Makes Eternal Lasting, who prefers the name his mother used for him: Born. They are sailing across a sea filled with kraken-like monsters which must be pacified by singing a lulling song. Riser approaches Born and instructs him to remove his Forerunner combat skin as it is upsetting the song. Born then consults with his armor's ancilla first; it is described as a disembodied intelligence, in a role similar to another famous A.I. It explains that electrical and magnetic fields, other than the ones caused by the planet's dynamics, throw the krakens into a frenzy, which is why the boat is powered by a primitive steam engine. She assures him that the armor will have no value to the human crew, so Born begins to remove his armor as the florian fetches him sandals made of reeds.
Born, who is a swap-member of the Builder caste in the Forerunner hierarch, shows the desire to turn his back on his future as a Builder and instead become a treasure hunter to search for long-lost Forerunner and Precursor artifacts. After exploring an island near a large crater, Born stumbles across a Forerunner Cryptum: a vault where Forerunners are interred in a state of neverending sleep and contemplation. Born encounters the AI monitoring the Cryptum and assumes that its occupant is to be revived. He hesitantly complies and reawakens the Forerunner inside. This Forerunner turns to be the Ur-Didact, a member of the dismantled Warrior-Servant caste who was interred in the Cryptum over a thousand years earlier. The Didact, upon awakening, assumes that his wife The Librarian (a member of the Lifeshaper class) sent Born and the humans to awaken him for some purpose. He takes Born and the two humans upon some recently arrived ships to retrace his steps prior to being put into the Cryptum, desperate to see if "it" was fired.
The four travel to a series of worlds that served as battlegrounds in the Forerunners' war against the humans, all of which show no signs of sentient or complex life, much to The Didact's dismay. He asks Born to accept a brevet mutation to gain some of the Warrior-Servant caste's traits and to allow access to his memories and those of his class, anticipating the urgency that his knowledge must not end with him. Born accepts, and gains access to the Didact's memories, learning that he holds deep regrets about his war with the humans.
The humans had been fighting a two-front war: one against the Forerunners and another against an extra-galactic threat known as "The Flood". The Flood originated as simple cells inside automated transports that made their way into the human's part of the galaxy. Initially they showed no noticeable signs of life or any sort of activity apart from making animals more docile. Humans and their allies, the San'Shyuum, used the spores on animals to domesticate them as pets. Eventually the pets began to mutate and become aggressive, as did the humans who handled them; the first variation of The Flood was born. The humans, fleeing their ravaged worlds, encroached upon Forerunner territory, who went to war as well. Although they lost to the Forerunners, the humans were able to defeat The Flood by injecting themselves with a formula that made their genetic material toxic to The Flood. The humans refused to tell the Forerunners how to beat The Flood when they returned.
The Didact then takes Born and the humans to the San'Shyuum's world where they have been in isolation since the end of the Human-Forerunner War. The cities are in turmoil as the Librarian's latest visit to procure "specimens" was seen as a sign for the San'Shyuum to rebel against the Forerunners. Some distance from the San'Shyuum's homeworld a portal appears and through it a large ring-shaped construct appears. The four are apprehended by the Master Builder, who is in the system to witness a test-firing of a new creation against the unruly San'Shyuum. Born is handed over to his family and escorted home. During his trip home the Didact's memory tells him that the creation of the ring-shaped construct, called Halo, was the reason he was placed in the Cryptum. He opposed their creation in favor of save-haven "Shield Worlds." Shortly after coming home, Born hears his father arguing with a member of the Forerunner council and decides to confront his father about the true nature of the Halos. He confirms that three-hundred years before, The Flood re-emerged in their part of the galaxy and the Forerunners were at a loss to combat them. He and the Master Builder decided to move forward with the construction of Halos. Each Halo has a powerful, energy-based weapon that can eliminate any life-forms with sufficient biomass to sustain The Flood in an entire star system. To his horror, Born learns that Halo was test-fired on the human worlds he visited (at low power) and the Master Builder recently test-fired another on the San'Shyuum's homeworld.
The Forerunner Council learns of the Master Builder's actions and summons Born to a criminal trial against him. High above the Forerunner homeworld sit eleven Halo rings, with one having been missing for many years. The trial is interrupted by Mendicant Bias, a rampant AI, who causes havoc with the Forerunners' computer and defense systems. Bornstellar and a group of others are rescued during the chaos in a small ship. Above them some of the Halo rings separate from the others and prepare to fire. The Forerunner fleet quickly assembles and begins attacking the renegade Halos, quickly destroying three of them, but a gigantic slipspace portal opens and allows the seven other rings begin to escape through it. Born's ship manages to escape through the portal before the Halos activate, wiping out all Forerunner life in that part of the galaxy.
Born is knocked unconscious during the slipspace jump and recalls The Didact's memories. He finds out (or remembers) that Mendicant Bias was an AI tasked with safeguarding the Halo constructs and overseeing their firing systems. After a test-firing over a human world, Mendicant Bias and the Halo disappeared with a much-feared creature held deep in a Precursor facility the humans had built over. Soon after, their ship arrives at the Ark, a "Shield World" located just outside of the galaxy where the Halo rings were constructed. There he meets the Librarian, who sees him as her husband now. According to her, the Master Builder had the Didact executed shortly after triggering the Halo above the San'Shyuum homeworld. They hypothesize that the creature that escaped from the Precursor prison somehow corrupted Mendicant Bias, who attempted to gain control of all the Halos but only succeeded with five. The rest, as well as The Ark, were co-opted by the Librarian as vessels on which numerous life-forms across the galaxy could live. The novel ends with Born recalling the Didact's contact with the captured lifeform: it revealed itself to be the last of the Precursors and was planning revenge on the Forerunners who wiped them out in ages past.