The John Keats cybrid that was killed in the previous book, Hyperion, has been given a new cybrid body and taken the name Joseph Severn. Because of his special relationship with the original Keats cybrid, the consciousness of which now resides in a neural shunt on the back of Brawne Lamia's head, Severn is able to see visions in his dreams of the events unfolding to Lamia and the other pilgrims on Hyperion. CEO Gladstone takes Severn on as an advisor so he may keep her informed of events on the planet of Hyperion.

The Ouster rebellion attacks the Hegemony of man at Hyperion. The Hegemony fleet is certain it will be able to defend the planet but is quickly proved wrong. CEO Gladstone has already been advised by the TechnoCore that the Ousters must be fought, for any attempt at arranging a peace will end with the annihilation of the human race. Gladstone commits the fleet to Hyperion and the Hegemony is immediately attacked in multiple locations by Ouster ships that had not been detected. With the bulk of the fleet massed at Hyperion, the Hegemony defensive response is too slow, and the Ousters begin bombarding the outer worlds. It quickly becomes apparent that the Ouster attacking fleets are not what they appear.

In fact, it is the TechnoCore that is behind the war. It is attempting to wipe out humanity and make way for an AI-created Ultimate Intelligence. The TechnoCore knows it will succeed in creating the UI because it has already been contacted from the future by the UI. But the message from the future also stated that humanity will also create a new Intelligence capable of fighting the TechnoCore's UI. Part of that Intelligence has traveled back in time and is hiding itself in the current events. The TechnoCore wants to help the future TechnoCore UI to flush out the human UI and deal a crippling or fatal blow to humanity.

Inevitably, the war is settled by events at the Time Tombs on Hyperion and the actions of the Hyperion pilgrims and the mysterious creature from the future known as the Shrike.