Following Boone's confrontation with Hegel that left him severely injured, he was eliminated by Zo'or. Beckett who was impregnated by Hegel gives birth to a boy who immediately grows up to a man. He assumes the name Liam Kincaid and goes to Boone's funeral where Quon would be eliminated by an alien replicant. After impressing Da'an he is made his new protector.
An exhibition, for the first arrival of the Taelons, showcases different artefacts. An artifact causes Liam to travel to an alternate time. Za'an questions how Da'an where able to join the Commonality. Za'an experiments with brain waves in order to cause aggression.
Liam and Augur are in a Taelon shuttle craft, when something happens they get thrown into a parallel universe. They discover that humanity is at war with the Taelons. They're taken by the rebels and discover that Sandoval's counterpart leads them. And Lili's works for the Taelons.
Augur is forced to take part in a Taelon experiment. Da'an and Liam try to convince Zo'or that altering minds and implanting humans to make them aggressive to fight the Jaridians is not the correct path. Maiya makes contact with Sandoval.
A Jaridian probe lands on Earth and begins sucking energy from the Comonality. The Taelons use humans in a near-death state to keep their connection while Lili and Sandoval try to find out what is draining the energy.
When large scale blackouts begin to occur in cities with portals, Taelon technology is blamed. Augur and Liam investigate the death of a portal worker by a strange creature that feeds on energy and is particularly attracted to the Taelons.
Siobhan falls while rock climbing. As the others search for her, she dreams that she is on trial for supporting the Taelons. Zo'or questions whether Sandoval's CVI imperative to serve the Taelons has broken down as others are experiencing.
Maiya experiences dimensional phasing. Augur and Liam believe they need to bring Isabel and Maiya together to let the universe merge them. Jonathan Doors announces his presidential candidacy and meets with Zo'or.
Dr. Belman's daughter does human testing on herself with an accelerant that causes her to rapidly evolve. Joshua Doors decides somebody should run against President Thompson in the election, somebody who will stand up to the Taelons.
Using Jiridian technology, scientists create a physical bio surrogates where a human consciousness can be transferred. When a surrogate escapes, they must find it before it uses its fighting and weapons knowledge.
A Taelon program offers a transformation into a younger, healthier version of oneself. Liam fears that something more dangerous is also happening. Lili is worried that Doors' run for the presidency is negatively affecting the resistance.
A mysterious death by poisoning creates questions about the safety of portal technology. When a Taelon is killed in the same manner, the investigation leads to a very smart scientist that even the Resistance was scared to work with.
A group of Resistance capture a volunteer from a Taelon program for youth. Liam decides they may learn valuable information from her. They also decide to send in one of their own as a volunteer to see what the program is teaching.
Lili is given a psychotropic drug called "bliss" via a Taelon device. They discover it is widespread. With an instantly strong addictive property, the addicts are dying within 48 hours. The investigation leads Liam and Sandoval to Ireland.
With a reporter on board, the Taelon mother ship is highjacked into interdimensional space. Liam is the prime suspect, causing an even bigger rift between Da'an and Zo'or. As the ship floats, lost in space, they must find the real culprit.
A shuttle crashes on a beach after being pursued by a second Taelon piloted shuttle. When Liam locates the survivor (a Taelon called Belleye), he claims to want to help the Resistance take back Earth from the Taelons.
Augur is recruited by a Taelon weapons project, but the others are worried about his involvement. When the project is launched earlier than originally planned to fight a Jiridian fleet, the Earth is in danger.
A Jiridian probe headed for Earth is shot down by the Taelon Embassy and crashes outside of D.C. Liam recovers the probe, but he, Augur, and Julia are captured by another underground resistance movement led by the real Colonel Liam Kincaid.
As the election draws near, Liam believes Zo'or is trying to have Jonathan Doors murdered. The Resistance worries that an attack is imminent at the final debate. Julia mobilizes a group to protect Doors against Liam's wishes.