In the Rise of Endymion, the conclusion to Dan Simmons's Hyperion saga, Raul Endymion and Aenea continue their flight from the forces of the Church and the Core. Raul sets off in search of the Consul's Ship, which they were forced to abandon, and Aenea, capable of infecting her followers with a vision of humanity's future, tours the Pax, gathering disciples. When the Church declares a holy war on Aenea's allies, the Ousters, Raul and she must reunite for one last confrontation with the corrupt Pope, with humanity's future hanging in the balance.

The Pope declares a holy war on the Ousters. Aenea decides that she must leave Earth and return to Pax space. She sends Raul back first, charging him with finding the Consul's Ship. Raul takes a kayak down the Tethys. On a world named Vitus-Gray-Balianus B, he is taken ill with a kidney stone and is nearly captured by a group of Core assassins, but is saved at the last minute by the Shrike and is able to pass through the portal to the next world. Eventually, he locates the ship and flies it to T'ien Shan where he is reunited with Aenea.

Aenea and A. Bettik had spent the time traveling to various worlds in the Pax. As she had done on each world that they visited, Aenea holds forums on T'ien Shan during which she discusses the ever changing relationship between humanity and the Core, preaches about the steps humankind must take to progress to the next level of evolution, and illuminates the dangers of Core technology, including the cruciform, which the Church has co-opted to grant its followers immortality, but whose use contains abominable consequences. At these forums, Aenea offers her blood for her followers to drink, telling them that it will infect them with the next steps of human progress.

Aenea and Raul are chased off of T'ien Shan by the Core assassins and journey to an Ouster Startree, but the rest is short-lived. The Church sends a fleet to attack the Startree and Aenea flees, dropping her disciples off on various worlds to act as leaders and visionaries for the local people.

Raul and Aenea then travel to Pacem where Aenea confronts the Pope. They are both arrested. Raul is placed in prison, and Aenea is tortured to death. The last moments of Aenea's life are witness by all of humanity as a shared vision, and the power of this vision breaks the hold of the Church on the people, who, led by Aenea's disciples, cast off their cruciforms and begin an open rebellion. As Aenea's disciples share her communion with the liberated population, all of humankind begins to awaken to a new reality and a giant leap of progress for all life occurs in the universe.