During the events of Hyperion , the pilgrims traveled to the Time Tombs while retelling their stories, which proved in each case to have been the storyteller's motive for participating in the final Shrike Cult pilgrimage. At the beginning of the novel, the pilgrims wait as a sandstorm occurs in the valley. Father Hoyt, hoping to die to relieve himself of the intense pain inflicted by his cruciform, staggers to one of the Tombs, the Jade Tomb. Here, he attempts to commit suicide, but is killed by the Shrike before he can do this. Brawne Lamia, who noticed Hoyt's disappearance, traces him to the Jade Tomb and encounters the Shrike. She fires at it with a pistol, but it is unharmed and disappears. Kassad observes these events quietly, hoping to lure the elusive female Moneta and the Shrike into his presence, so that he may confront and potentially kill them.
The surviving pilgrims demand that the Consul command his AI-controlled starship to come to the valley, supposedly so that they can use the medical supplies on board to attempt to save Father Hoyt, who has lost too much blood and is nearing brain death. The Consul is reluctant to do so, but he finally relents, only to find that the ship has been placed under interdict by Gladstone and the Hyperion authorities. They decide to take refuge in the Time Tombs from the storm. Meanwhile, Kassad begins to follow the other pilgrims into the tombs and is attacked by a mysterious sniper he assumes to be Moneta. In response he lays waste to one of the tombs called the Crystal Monolith, where the last shots had originated. He rushes the damaged tomb while under heavy fire that destroys his armor and enters, ignoring the attempts of the other pilgrims to contact him. The next morning the remaining members of the pilgrimage wake to find that Father Hoyt's body had been resurrected into Father Paul Duré. The Consul provides his notes of the group's stories to Duré to bring him up to speed.
Kassad finds Moneta at the top of the Obelisk. She does not remember him as she has moved backwards in time since they met. He attempts to shoot her but his gun will not work in the crystal tomb. As he wrestles with her, attempting to kill her, she continues to ask him why he wants to kill her. They fall to the floor below and she dons the quicksilver armor. Kassad makes a killing blow with his power suit, but it is ineffective against the strange armor. After ripping his armor off and knocking him senseless she rapes him. Afterwards she takes him into the tomb and gives him the quicksilver armor. The Shrike appears and takes him through a portal it created in the air.
After searching the tombs once more for their missing people, and running low on food, the pilgrims delegate Lamia and the poet Martin Silenus to travel to Keep Chronos and the Poets' City, respectively, to find food. Silenus goes to the Poets' City to complete his "Hyperion Cantos", but is instead surprised by the Shrike and impaled on the Tree of Thorns, which is revealed to be partially real. Lamia, at Keep Chronos, recovers the necessary supplies and returns to the Valley, but is also attacked by the Shrike and loses consciousness. She awakens at the fringe of the TechnoCore, in one of its computerized realities, in the company of her implanted John Keats persona. Lamia and the Keats persona converse with a major AI named Ummon, which reveals some of the motivations of the TechnoCore and the existence of a war between human and AI ultimate intelligences. As the conversation concludes, the Keats persona is killed by Ummon, and Lamia is released into unconsciousness.
Kassad finds himself with Moneta, overlooking the city of Keats while the Ouster invasion force lands on Hyperion. She explains that it is 5 days in the future and that the Lord of Pain can be controlled by one who defeats it in single combat. Without hesitation, Kassad agrees to fight the Shrike, hoping to gain control of it and use it in the ongoing war. He is transported to a future Hyperion where the planet is desolated and without atmosphere, and all that remains is the thorn tree, the tombs, and hundreds of Shrike creatures. Vowing to save all the victims impaled on the thorn tree, Kassad charges the first Shrike that had appeared to him.
Father Paul Duré decides to wait with Sol Weintraub and Lamia's now-recovered, but unresponsive, body, while the Consul uses his hawking mat to fly to Keats, in an attempt to use his former leverage and political connections to free his ship. Instead, the Consul crashes on a river miles from Keats and is taken captive by two thieves. He only escapes death due to the personal intervention of his protégé, Governor-General Theo Lane, with whom he returns to the capital. At the Tombs, True Voice of the Tree Het Masteen reappears mysteriously, revealing Shrike Cult collusion with the Templar Brotherhood beforedying and claiming that he and the erg creature he brought with him in the Mobius Cube were to pilot the Tree of Pain through space and time. Shortly thereafter, Father Duré leaves Sol, ostensibly for a "walk," and disappears.
Minutes before the time of Rachel's birth and the simultaneous "opening" of the Time Tombs, Sol brings the baby Rachel to the foot of the Tomb known as the "Sphinx," where she is received by the Shrike, who carries her into the building.
Severn's character, the second "cybrid" of John Keats, is introduced at the beginning of the novel, at a formal event at Government House on Tau Ceti Center, the primary world of the Hegemony. Here, he claims to be an artist attached to Gladstone's staff in an attempt to provide an artistic view of the beginning of the war for Hyperion, which is under attack by the Ousters. At the event, senior Hegemony officials observe a FORCE fleet departing for the Hyperion stellar system, after which Severn accepts the invitation to dinner of a colorful socialite, Lady Diana Philomel.
After the dinner, Severn, intoxicated, is seized by Philomel, her husband, and several associates, who incompetently attempt to coerce Severn into providing classified information. They are interrupted by Hegemony security personnel, who arrest Severn's captors, revealed by Gladstone as royalists with connections to the Shrike Cult. Severn next observes meetings of both the Hegemony cabinet and Gladstone's inner circle, updating Gladstone on the Hyperion pilgrims while still pretending to be an artist.
Suddenly, while touring several farcaster-connected worlds between meetings, Gladstone is informed that the Ousters have counterattacked, attacking the WorldWeb itself in an unprecedented and unexpected move that appeared impossible. Since FORCE strategic reserves have been committed to the war in the Hyperion system, the first wave of worlds threatened by the Ouster invasion seem destined to fall. Severn tours several of the worlds, narrowly escaping from a rioting mob that recognizes him as one of Gladstone's associates. As sudden Shrike Cult uprisings devastate major Hegemony planets, Keats travels to Pacem, the homeworld of the Catholic Church, where he encounters Father Duré. Duré had disappeared from Hyperion after entering the planet's underground labyrinth, and was escorted by the Shrike through various places and finally to Pacem, where he sought out his old confidante, Monsignor Edouard, and described the events that he experienced in the past years. Duré, intrigued by the collusion of the Templar Brotherhood with the Shrike Cult, travels to God's Grove, the Brotherhood's home and soon to be within the range of the Ouster invasion armada. Severn, accompanied by Gladstone's aide Leigh Hunt, farcast to Tau Ceti Center, but instead arrive on a world that isan apparent analog of 19th century Earth and, in particular, the city of Rome, where the historical Keats died. Like the original Keats, Severn contracts tuberculosis and his physical form dies, but his persona retreats into the computerized realities of the TechnoCore.
The Consul meets with the leaders of the Ouster Swarm attacking Hyperion, which is on the verge of falling to the siege. He is tried for the murder of the Ouster agents he killed years previously, but is not punished, his sentence being to live during the turbulent times that the Ousters believe shall follow the war (a sentence the Consul later compares to the "old Chinese curse", commonly stated as 'May you live in interesting times'). The Consul is then informed that there is no Ouster offensive against the WorldWeb, and concludes that the TechnoCore is the only power capable of launching such an attack. The Ousters then offer their support to the Hegemony in their struggle against the artificial intelligences of the TechnoCore, but only in the form of retaliation for the fall of the Hegemony, which they claim is inevitable since the Ousters refuse to use farcasters.
Gladstone, who has resolved to use a TechnoCore device against the Ousters while Hegemony citizens temporarily evacuate and retreat into the labyrinths of the worlds containing those features, is sent this information, and also discovers that a FORCE autopsy of Ouster bodies found during a failed counterattack against the invasion armada reveals that the "Ousters" are truly TechnoCore androids. Gladstone retires for a brief time, and, while napping, is approached by Severn in a dream. Having met with his creator, Ummon, Severn has discovered that the TechnoCore resides within the farcaster system, fearing alien intelligences (Lions and Tigers and Bears) to be found in the Void Which Binds, a reality thought of by the Hegemony as a communications medium. Gladstone orders the immediate destruction of the farcaster network, knowing that, despite the inevitable death and chaos that will follow this action, it would cause a cessation of TechnoCore activity. She does so, and resigns as chief executive.
Back on Hyperion, Brawne Lamia, who has awakened from her coma-like state, penetrates the Shrike Palace to find Silenus and all of the other victims of the Shrike connected via a long cable. She manages to free Silenus, just as the Shrike appears and prepares to attack her. She mysteriously manages to freeze the Shrike as it advances, and it falls over a precipice and shatters. Meanwhile, Sol's daughter Rachel appears in a newly formed body outside the Time Tombs as a young woman, carrying her younger self (now aging normally again). Giving her younger form to Sol, she explains that she is Moneta, and is now traveling back in time with the Shrike under orders from humanity's future. She disappears and Sol decides to go forward in time to Rachel's future using the portal.
Elements of FORCE discover that the TechnoCore invasion has suddenly ceased, and that the invasion armada lacks any personnel whatsoever. Throughout the former WorldWeb, chaos breaks out, with shocked Hegemony citizens turning to violence. On Tau Ceti Center, Government House is besieged by a furious assembly of citizens. Gladstone allows herself to be killed by the demonstrators, remaining on the planet even after her de jure successor, Senator Gabriel Kolchev, flees. In addition, the entire fatline communication relay is suddenly shut down by unknown forces, the final broadcast to every receiver being that access has been revoked until humanity is ready to properly use it.
The story concludes several months later; the worst of the chaos caused by the fall has abated, and Hyperion is flourishing again, with former Hegemony citizens and Ousters co-existing. Newly substantiated glyphs give some insight to the various tombs and monoliths of the Time Tombs, and, rarely, the portal to the future will admit a person. The novel ends with the Consul returning to the former Web Worlds in his starship to discover what happened, with Severn's artificial intelligence stored in his ship.
The novel Endymion is set 274 years into the future in the same universe. It contains references to several of the characters in the original Hyperion cantos and their future life after the events depicted in The Fall of Hyperion .