Hyperion tells the story of 7 pilgrims who have been asked to travel to Hyperion to seek out the Shrike, a mysterious creature that lives in a region known as the Time Tombs. The pilgrimage is critically important because a group of outcast humans known as the Ousters are on the verge of attacking Hyperion, and it is feared what may happen if they control the Time Tombs and the Shrike. The seven pilgrims are the priest Lenar Hoyt, the soldier Fedmahn Kassad, the poet Martin Silenus, the Templar Het Masteen, the scholar Sol Weintrub (and his infant daughter Rachel), the private detective Brawne Lamia, and the Consul.

The pilgrims gather together on the tree ship of the Templar prior to descending to Hyperion. There, they decide to each share their story as they continue their journey in order to better understand why they were chosen for the journey and to, hopefully, learn what they can about the Shrike in order to complete their pilgrimage successfully. They draw numbers for the order to tell their stories, and Father Hoyt is first.

The Priest's Tale: Father Hoyt's story actually involves another priest, Father Dure, and is told via excerpts from Dure's own journal. Dure, after being exiled by the church for falsifying evidence of Christianity on other planets, decides to go to Hyperion in search of the Bikura - a group of humans that had crashed on Hyperion hundreds of years ago, forming their own small culture. He finds them, 70 to be exact, but they murder his companion in the night, sparing Father Dure because he "follows the way of the cross". Ultimately, it turns out that these Bikura are the same who crashed 400 years ago, but they have been kept alive by a creature (in the shape of a cross) that has adhered itself to their flesh. Father Dure is also given one of these to make him "of the cruciform".

When he attempts to flee to share his discovery, he learns that it is impossible to travel more than a few km from the Bikura village. Realizing this, he drags himself into the Tesla trees (lightning trees) and attaches his body permanently to a tree. As a result, he is "killed" over and over again by the lightning, but kept alive by the cross creature. It is in this state that Father Hoyt finds him, seven years later. Unfortunately, he too has been infected by a creature, and the cruciform of Father Dure attaches itself to Father Hoyt. The Consul is the only one to learn this fact, and Father Hoyt must constantly administer high doses of pain medicine to deal with the pain of being away from the Bikura village (which has been destroyed).

The Soldier's Tale: Fedmahn Kassad tells a story of how he is visited by a mysterious woman throughout his virtual soldier training. During each of these visits they have sex, but do not speak much otherwise. Years later Kassad crashes onto Hyperion, where he is found and tended to by his mystery woman (Moneta). She reveals to him that the Shrike and Time Tombs are travelling backwards through time. Together, they go to the Time Tombs and, with the Shrike, destroy the Ousters that had followed Kassad to Hyperion to try to kill him. After the fight, while having sex with Moneta, he realizes that she is the Shrike, and he pulls away just before he is killed. Kassad also reveals that he saw on the bodies of some (or all?) of his companions on the Shrike's thorn tree.

The Poet's Tale: Martin was on Old Earth just before it was destroyed. He was sent off planet by his mother, but became brain damaged during the journey. After years of writing bad novels for quick cash, Martin foregoes his lucrative career to pursue more artistic avenues in Hyperion. While there, the Shrike murders many other citizens, but it is the Shrike who becomes his muse. After all others have fled or been murdered, Martin us unable to finish his Cantos. Thus, he leaves Hyperion to travel at relativistic speeds in order to return at some point when the Shrike is active again so he can continue his great poem.

The Scholar's Tale: Sol Weintraub's daughter Rachel was studying the Time Tombs on Hyperion when a mysterious event caused her to get younger every day, and to slowly regress in memory as well. Sol and his wife began having dreams to go to Hyperion to sacrifice their daughter as a blood offering (a la the tale of Abraham and Isaac). While Rachel gets younger and younger Sol seeks help from the Shrike church, but they will not meet with him once they learn of Rachel's ailment. Thus, 24 years later and after the death of his wife, Sol is now taking his infant daughter Rachel to the Shrike in the hope that he can reverse the ailment that will soon kill her (or at least cause her to cease to exist).

There is no tale for Het Masteen as he disappears in the night while crossing the Sea of Grass. Though his room is covered in blood, they do not find a body and so it is not certain he is dead.

The Detective's Tale: Branwe is approached by Johnny (a cybrid - a human body that is embodied by an artificial intelligence that is a member of the TechnoCore). Johnny was murdered - his cybrid body was destroyed and part of his memory was lost. During the investigation, Johnny learns that the Shrike is either a future creation of the TechnoCore that was sent back through time as a preemptive strike to destroy humans, or as a future creation of the Ousters that was sent back through time as a preemptive strike against the TechnoCore. Johnny (who , it turns out, is a recreation of the poet John Keats) puts all his AI existence into the human body in order to free himself of the Core with the intention of travelling to Hyperion. Unfortunately, he is killed while attempting to flee (with the help of the Shrike Church). Brawne, now carrying Johnny's child and his memories on a data chip, survives.

The Consul's Tale: The Consul's tale begins by telling how his grandfather, Merin, met and fell in love with a woman named Siri on an early colonization planet. He was a crewman on a ship, and she remained on the planet, causing her to age over 60 years while he aged only a few. When she dies, he finds that she secretly opposed the construction of a farcaster (a portal to travel instantaneously between worlds) and she gives him the tools to start a rebellion. He does, bringing about the Siri Rebellion. Though a bureaucratic agent, the Consul was also still fighting against the Hegemony, only in more subtle ways. In meetings with the Ousters, the Consul reveals all the Hegemony secrets he knows. As a result, the Ousters tell him they can control the Time Tombs and free the Shrike. Learning this, the Consul kills his Ouster companions and begins the process that will free the Shrike, effectively rendering the pilgrimage pointless. In spite of this, the companions all agree to continue, and the book ends with them all walking hand in hand on the path to the Shrike while singing "We're off to see the Wizard"¦"