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Halo: Cryptum is the first novel in The Forerunner Saga by Greg Bear. The novel explores Forerunner society and their shared history with humanity. The story is told in a first-person narrative, from the perspective of a Forerunner Manipular known as Bornstellar Makes Eternal Lasting, and follows Bornstellar's adventures with the ancient Promethean military commander known as the Didact and two humans, Chakas and Riser.
Bornstellar Makes Eternal Lasting is a young Forerunner Manipular who refuses to follow in his father's footsteps and become a Builder. Bornstellar's rebellion prompts his father to send him to live with the Miners, a rate lower than Builders. After living with the Miners on Edom in the Sol system for some time, he is inspired by his assigned ancilla to hunt for artifacts left by the Precursors — beings of extraordinary power that preceded the Forerunner civilization.
Bornstellar escapes to the nearby world of Erde-Tyrene, the ancient homeworld of the human species and their last repository after the humans' ancient spacefaring civilization lost a devastating war to the Forerunners who devolved them and exiled them on their homeworld as punishment. Erde-Tyrene was then left under the stewardship of the Forerunner Lifeshaper, the Librarian, whose guidance allowed the humans to begin an arduous process of recovery. On Erde-Tyrene, Bornstellar crosses paths with two humans - Chakas and Riser, who guide him on his search for Precursor artifacts. In the Djamonkin Crater, they find an artifact that is revealed to be a Cryptum — a "warrior keep" created by a Forerunner Warrior-Servant group known as the Prometheans, guarded by ancient war sphinxes.
To Bornstellar's surprise, the Cryptum is unlocked by a code the humans had been unknowingly programmed with. Upon opening the Cryptum's seal, Bornstellar finds that it belongs to an ancient military leader known as the Didact, who is then unwillingly revived from his millennial hibernation. Some days after the Didact's revival, a fleet of Forerunner ships arrives in the area, apparently aware of the Didact's presence despite the baffler that hides the central region of the crater. The Didact realizes that the ships have arrived to ask for his help in something that is at this point unclear to Bornstellar. However, the Didact has other plans. He deduces that his revival, Bornstellar and the humans were part of a larger plan engineered by the Librarian, his wife. He decides to make his escape using a ship created from a design seed planted under the crater's central peak, taking Bornstellar, the humans and his war sphinxes with him.
They jump into slipspace and make their way to the formerly Precursor-occupied world Charum Hakkor in a distant system, where they find that every Precursor structure has been destroyed and that a mysterious entity that had once been imprisoned on the planet is nowhere to be found — something that greatly troubles the Didact. Further scans of the system reveal that all neurologically complex life in the entire system, including the planet Faun Hakkor, has been eradicated some decades prior.
Shortly afterward, they travel to the system where the San'Shyuum species — humanity's former allies — had been quarantined after their war with the Forerunners, in order to meet the San'Shyuum elders and find answers by triggering the humans' ancestral memories the Librarian had imprinted them with. In order to access the quarantine system, they meet the Confirmer, a Promethean who once served alongside the Didact and has now been placed in charge of the San'Shyuum. Before they arrive, Bornstellar undergoes his first mutation from Manipular into first-form, acquiring the genetic imprint of the Didact. After meeting with the Confirmer on his Fortress-class vessel Deep Reverence, they travel to Janjur Qom, the San'Shyuum homeworld.
As they approach Janjur Qom, it becomes apparent that they have walked into a trap engineered by the Didact's ancient enemy, the Master Builder. The world is in ruins, swarming with Forerunner ships and war machines; the San'Shyuum have attempted a rebellion that is now being violently suppressed. The Didact's ship is swiftly intercepted and dismantled by a superior force of Forerunner warships and its occupants are captured and taken aboard the Master Builder's ship. Before this, Bornstellar witnesses a Halo ring transition over the San'Shyuum world. Bornstellar is then questioned by the Master Builder, but has few answers. Frustrated, the Master Builder sends Bornstellar back to his family, while the Didact and the two humans remain in captivity.
Bornstellar is sent to the Orion complex, where he is reunited with his family. On their homeworld, he studies Forerunner history and discovers the Master Builder's plan to gain more power and to diminish the role of the Warrior-Servants — a scheme that has been in motion since conclusion of the Human-Forerunner wars. This plan involves removing the Warrior rate from the Ecumene Council, and a Builder weapon that would make all other weapons obsolete — Halo. Over time, Bornstellar also finds that the Didact's memories and consciousness — gained as a byproduct of his mutation — are slowly gaining more and more prominence within him, with the Didact occasionally making comments and observations in his mind.
One day, exploring his family's vast domicile, Bornstellar overhears his father and another Builder conversing in secret. It is revealed that the Master Builder activated the Halo ring at Janjur Qom, as punishment for the San'Shyuum rebellion. The Council disapproves of this use, considering Halo installations as weapons of last resort. They also discuss a missing Halo ring that was tested near Charum Hakkor. Further complicating this is the fact that a powerful, metarch-level ancilla went missing with it. The next day, Bornstellar confronts his family with a message from the Didact within. He reveals that he knows of the missing Halo installation, and that it released the creature imprisoned on Charum Hakkor. Bornstellar's father, the designer of the Halo rings, is at first reluctant to discuss the matter, but reveals that Bornstellar has been asked to come to the Forerunner capital to testify against the Master Builder in a trial held for his violation of the Mantle.
Aboard the Council ship Seedling Star, Bornstellar meets Splendid Dust of Ancient Suns, a young first-form councilor who instructs him and gives him access to historical records. During the journey to the capital, Bornstellar studies the background of the Flood and discovers that the parasite was defeated ten thousand years ago thanks to the efforts of the humans, but has now resurfaced in the Forerunners' domain, attacking a number of bordering worlds over the last 300 years. He also learns that following the war with the humans, there was a millennia-long political strife between the Builders and the Prometheans, with the Didact proposing a strategic solution, the building of fortresses known as Shield Worlds to monitor and control potential Flood outbreaks. On the other hand, an extreme faction of Builders led by the Master Builder began designing a superweapon which could decimate life on a galactic scale. The Builder faction was victorious and the Prometheans were forced out of the council, with most of them going into exile.
The Master Builder's trial takes place in the Forerunner capital, a massive construct now orbited by the remaining eleven Halo installations. The trial is interrupted by the rogue Contender-class AI Mendicant Bias, who launches an invasion on the capital using the twelfth, "lost" Halo installation, also taking control of five of the other rings in an attempt to fire them and sterilize the capital system. With the help of the knowledge of the Didact's consciousness within, as well as the Warrior-Servant known as Glory of a Far Dawn, Bornstellar and Splendid Dust of Ancient Suns escape the chaotic battle around the capital through a slipspace portal in an escape pod.
The portal takes them to the Ark, the place of construction for the Halo rings and the Librarian's base of operations. At this point, Bornstellar finds that he has become more and more detached from his original self, while the Didact's personality is much more prominent than before. Splendid Dust of Ancient Suns inquires the Didact within Bornstellar about the missing Halo and Mendicant Bias. It is learned that the disappearance of the AI and the ring may be connected to the creature once held captive on the planet. After drifting in space for some time, they are rescued by a Lifeworker ship and given medical care.
Once Bornstellar has recovered, a meeting between him and the Librarian is arranged. To Bornstellar's surprise, the Lifeworkers and the Librarian treat him as an incarnation of the Didact; the Librarian reveals that on Janjur Qom, the Didact refused to give the Master Builder information on how to control the Contender-class intelligences or where the Didact's Shield Worlds were located. As a result, the Didact was evidently executed, making his imprinted consciousness within Bornstellar all there is left of him.
Bornstellar–now the Didact–and the Librarian spend time together on the Ark, inspecting all the species she has gathered from across the galaxy. Due to the Flood's return, the Didact assumes the role of the commander of Forerunner military once again, preparing to reactivate the Shield Worlds and the defenses he had planned thousands of years earlier. There is no knowledge of the status of the Forerunner government or the remaining Halo rings. The Didact also ponders on the status of Chakas and Riser, suspecting that the humans may have been spared by the Master Builder if he realized their value; their genetic memories contained the answer to defeating the Flood. Now, the Didact seeks to find the lost Halo ring, controlled by Mendicant Bias, and the captive from Charum Hakkor. In the end, the Didact recalls what the captive said when he communicated with it thousands of years prior; the entity revealed that it was in fact the last Precursor, and that the Forerunners had been created by its kind millions of years ago, before they "ruthlessly destroyed" their creators. Finally, the being ominously stated that "their answer is at hand."
Halo Waypoint features a glossary of nouns used in Halo: Cryptum to make sure readers understand the meaning of the terms and phrases used in the novel. A note at the beginning of the novel states that, like in Halo 3's terminals, many elements are modified to be intelligible to the reader, though not necessarily in English, (viz. geas, Faber, Manush). Thus, these terms and phrases should be interpreted as representative rather than literal.