Joseph Severn is the second John Keats personality reclaimed by the TechnoCore, and all of Fall of Hyperion is told from his perspective. When he is with Meina Gladstone it is in first person, but while he sleeps he dreams of the events of the pilgrims on Hyperion, at which time it transitions to third person. For the sake of the synopsis I will separate the summary of what happens to the pilgrims and what happens to CEO Gladstone and company.

On Hyperion the pilgrims have been in the valley of the Time Tombs for over a day without meeting the Shrike. Things begin to happen rapidly the next day, however, when Lenar Hoyt is killed by the Shrike, and Paul Dure is recycled by the cruciform creature. Running out of food, Brawne and Martin head back to Chronos Keep to gather supplies. Martin stops at the City of Poets where, while finishing his poem, he is taken by the Shrike and put on the giant tree of thorns. Meanwhile, Kassad is taken by Moneta and the Shrike through time, and Kassad challenges the Shrike to a fight. He is wounded while fighting and taken into the future where he is healed by a group of Ousters (who we learn use genetic modification to alter their appearance and to make them suitable to harsh environments).

The pilgrims discover Het Masteen in the valley. He had made a bargain with the Shrike Cult to be the pilot of the tree of thorns through the galaxy. Upon seeing it, however, he was unwilling to do so, and thus he died. The Consul, Father Dure, and Sol Weintraub decide that they must use the Consul's ship to save Rachel (by putting her in fugue) since she has little more than a day until her actual birthday. The Consul takes the Hawking Mat (flying carpet) his grandfather had used and begins a journey back to the city of Keats and his ship. Just north of the city the mat loses power and crashes. Meanwhile, Father Dure leaves Sol and journeys into a Cave Tomb, where he finds himself in one of the 9 underground labyrinths. It is full of millions of cruciforms and even more dead humans. The Shrike pulls him from there and into a ship where he removes Dure's cruciform and farcasts him to the planet Pacem.

Sol has a vision that it is Rachel who wants him to give her to the Shrike. Realizing she only has seconds to live, he does so, and the Shrike takes her into the Sphinx Tomb. Brawne returns with the supplies, but is incapacitated when she is hooked up to the Sphinx Tomb via her neural shunt. She and Johnny (the original Keats persona) travel to the core where they meet Ummon who tells them that the Shrike may have been created by either Ousters or the AI. It also tells them that there is a human God that evolved from their consciousnesses in the future, and then was it all times, and that there was a god (ultimate intelligence) created by the AI that had the same outside of time qualities. The AI UI tried to kill the human UI, but the human God was made up of 3 parts and the third (Empathy) has traveled back in time to flee the battle. It is, we learn, among the group of pilgrims. Johnny is killed by Ummon but Brawne is sent back to her body.

Sol, alone now, finds Brawne emerging from the Jade tomb. On her return from meeting Ummon she learned that Martin was on the tree of thorns and that there was a connection between it and the Shrike palace. She travels there, where she is able to find and free Martin from his suffering. The Shrike approaches her, but (at the bidding of Moneta) she walks on air and pushes it down, causing it to shatter like glass. Martin and Brawne return to Sol. After his healing, Kassad attacks the Shrike again, knowing he will die. They travel in time again, this time to a great battle between the Ousters and thousands of Shrikes. They are victorious, but Kassad dies and is entombed within the Crystal Monolith in the future.

The Consul is saved by Theo Lane and with Arundez (Rachel's lover 50 years ago) they take his ship and meet with the Ousters to negotiate. They learn that the Ousters are not invading any planets other than Hyperion, and they relay that information to Gladstone. They then return to the Time Tombs.

CEO Gladstone learns that the Ousters are not only invading Hyperion but are invading the web itself. Realizing they cannot save all their planets, they decide to sacrifice the first wave, and pull back to concentrate their forces. Many planets are destroyed utterly. With the aid of Severn's visions and information from Father Dure (who contacts her after ending up on Pacem) they learn that the so-called Ouster invasion is actually made up of Cybrids created by the TechnoCore. Joseph Severn, on his way back from Pacem with Father Dure, is transported to Old Earth instead. He soon dies from consumption yet again, just as the real John Keats had. After his death, however, his AI consciousness meets with Ummon and learns that the core resides in between farcaster portals. He passes this information on to Gladstone via a dream.

Gladstone has all farcaster portals destroyed instantaneously to rid humanity of the AI threat, knowing full well that millions will die without the necessary food and supplies that are transported via farcaster. They are successful, though, and the AI threat is stopped.

Meanwhile, the Severn/Keats AI persona travels to the Sphinx tomb where, by using the erg brought by Het Masteen, he is able to grab the infant Rachel out of the Shrikes hands. He holds her there until Moneta comes through and takes Rachel back out to her father. It is now we learn that Moneta is actually a grown Rachel who was prepared to be the keeper of the Shrike through her Merlin's sickness. Sol and infant Rachel travel through a portal in the Sphinx to the distant future where Sol will raise her among Ousters in training for her future duties. We also discover that the child Brawne is pregnant with is the Empathy part of the human God, and it will become a great teacher of the universe. Brawne and Martin remain on Hyperion (it is implied they are living together, though it is not stated explicitly). The Keats AI persona now resides in the Consul's ship. Father Dure is named the next Pope.