As "Shift" by Hugh Howey begins, the year is 2049. Democrat Donald Keene has just been elected to Congress. He is heading to Washington to serve his term and meet with Georgia’s Democratic Senator Thurman. Keene’s background in architecture and his college design of underground silos prompted Senator Thurman Keene to recommend him to work on the Containment and Disposal Facility project, or CAD-FAC. CAD-FAC is being designed to store the world’s spent nuclear fuel, and it will consist of dozens of underground silos. Keene agrees to work on the project, though he isn’t happy about the recommendation coming from Keene’s daughter, Anna. Anna and Keene dated while in college, a fact which makes Keene’s wife, Helen, uncomfortable.

CAD-FAC is completed in Georgia several years later. The land above the silos plays host to the Democratic National Convention. During this time, nuclear blasts are detonated. Keene and selected others are rushed below ground into CAD-FAC. It is revealed CAD-FAC’s true purpose is to save humanity against total destruction. Thousands of people are put into the silos that extend miles below ground to live out their lives over the course of five hundred years while the earth becomes hospitable once more. The central silo, Silo 1, houses shifts of people from the old world, including Thurman and Keene. They are awakened every few decades from cryogenic sleep for six months at a time, where they oversee control and monitoring of the other silos. From time to time, rebellions and widespread violence in the silos cause the populations to be exterminated and replanted.

Keene is sickened by the knowledge that the entire operation was a conspiracy and by the knowledge that Thurman and his group set off the nuclear blasts themselves. Thurman explains that it was necessary due to the rise of nano-terrorism. He goes on to say that it would only have been a matter of time anyway before a catastrophic event occurred. Good people had developed cell-sized nano-medical bots to heal and repair the human body, but terrorists and thugs like the Iranians weaponized them to tear people apart. Thurman jumped ahead by killing billions with nuclear weapons, but saving thousands to restart the world’s population all over again in five hundred years. Keene is horrified by what has happened, but knows he must now ensure as many people as possible survive in the other silos. Every few decades, silos must be restarted. Others go offline completely and cannot be raised.

In Silo 18, a revolution begins. Seventeen year-old Mission finds himself caught up in the middle of the violence, but he is given a reprieve. Instead of being killed, he has his mind wiped. He is allowed to marry and have children. In Silo 17, an uprising results in the population collapsing on its own, leaving a handful of survivors, including Jimmy. Jimmy lives for years at a time without seeing anyone. Meanwhile, Keene uncovers more secrets about the silo project. He kills Anna for her part in things. He then discovers the true goal of Thurman and the other founders. Only one silo out of dozens is to be released back into the world. All others, including Silo 1, are to be exterminated. Thurman explains this is in order to eradicate bad knowledge about nano-technology and nuclear weapons of the old world. Keene then kills Thurman. Keene learns that a single female has escaped one of the silos and has headed toward another. This woman, Juliette, becomes the first person who Jimmy sees in years. Juliette radios in to Keene, telling him she has begun to uncover the truth about the silos and that they will be coming for Keene.