Nine hours after Beckett conceived, her child is born. The Resistance must decide what to do with Beckett and her rapidly developing child, Liam Kincaid, who reaches maturity within minutes of being born. Sandoval reveals Boone's ultimate fate to Lili. Rayna transmits a signal to the Jaridians, an alien race. A Jaridian probe replicant assassin is set to destroy all Companions. At Boone's funeral the Taelon Synod leader, Quo'on, is assassinated, but Liam saves Da'an. Da'an appoints Liam as his personal protector. Zo'or realizes that if the replicant kills Da'an, then he'll be made synod leader by default.

Augur taps into the Taelon Commonality, breaking Da'an's contact with the Commonality. Da'an regresses into the "Atavus", a pre-historic version of the Taelons. Zo'or tells Sandoval to kill Da'an. Da'an is a threat for the Atavus only has a hunger for life spirit. The Resistance lures the Atavus to try to save Da'an.

At an exhibit of Taelon items from Strandhill, Liam jumps through a Taelon portal which takes him two days into the future, where he finds everyone in the Resistance headquarters murdered. On returning to the present, he races to stop the massacre and begins to suspect that he is the assassin. Zu'or attempting to destroy Liam, beams dangerous brain wave emissions to him from the Taelon mothership. Doors, highly suspicious of Liam, becomes agitated and demands that Liam be shot.

Liam and Augur are thrown into a parallel dimension when their shuttle flight is sabotaged by Doors. Maiya captures them and brings them back to her Imerian Resistance camp, where they start to find counterparts of people they know. The counterpart Taelons capture the colony and takes them to the mothership.

Augur is arrested for treason in Russia and condemned to death by hanging. However, he is blackmailed into participating in a Taelon experiment as advanced warriors and is implanted with a CVI. Maiya confuses Sandoval for her lover, Jason, from her dimension thus attracting Sandoval. For protection, Maiya takes the identity of Isabel Martinez. Liam helps Augur break his CVI and bring him back from the rage. Lazarus, the overseer of the program, was brought back to normal by Da'an.

A Jaridian probe crashes into earth and disrupts the Commonality, leading the Taelons to round up suspected Resistance members to be harvested for their life force energy to feed the draining Commonality. As Augur, Maiya and the others lie near death, their souls are in a dream world. Liam, in a comatose state, finds them and tries to bring them back, but they are happy in their dreams and refuse to return. Lili and Sandoval locate the probe in Australia.

Working on the New York to Bangkok inter-dimensional link, a technician is killed by energy-eating creatures. Liam and Augur suspect the creatures may be from another dimension, and will drain every energy source on earth. The mothership becomes infested with the creatures, leading the Taelons to put themselves into a near-death state to protect themselves.

Beckett's CVI begins to break down, causing her to slip and fall while climbing in a cave. Unconscious, she hallucinates a trial for her crimes against humanity and for collaborating with the Taelons. Liam and Augur try to find Becket before Sandoval finds and kills her.

Maiya begins to suffer from dimensional phasing, Augur claims that Maiya and her counterpart Isabel must merge or they may both die. Doors enters presidential race to begin to challenge the Taelons. Lili confirms that Isabel and her have the same father. Sandoval questions Maiya on the mothership, while Doors and Zo'or discuss joining forces.

Dr Belman and her scientist daughter Joyce inject an injured ape with the serum, regenerating its injured organs. Unlike her mother, Joyce is eager to try the serum on a human subject.

Lili is taken hostage as a Jaridian escapes from the Taelons in a shuttle. Liam pursues and both shuttles are drawn into a alien vessel. Liam explains that the vessel is a repository for the Kimera's accumulated knowledge. In order to leave, they must go to the vessel's core. Da'an confronts Zo'or about the Jaridian's escape, and challenges his authority. The Jaridian reveals his race and the Taelons were one until the Taelons separated. Now the Taelons want to force a union with the Jaridians by using humans as soldiers against them.

With Da'an's help, a handicapped scientist genius, Sparrow, heads a program where disabled persons can transfer their consciousness into a healthy body by creating a biosurrogate with Jaridian replicant programming, and then live normal lives. A reporter sneaks into the lab and his camera flash activates a biosurrogate. Sandoval arrives to find the reporter and a guard dead, and the biosurrogate gone having no consciousness of it's own. Lili finds that Zu'or has tampered with Da'an's research and have programmed the biosurrogates into killing machines. Liam learns that Sparrow has transferred his consciousness into a second biosurrogate.

Zu'or sponsors a "fountain of youth" program, called Second Chances, which makes old and ailing people young again. The resistance are trying to replace Doors as leader. Pearl Bell says that she had no previous use for the Taelons before she undergoes the first public transformation. While being interviewed afterward she states how Taelons had before helped her son live. Resistance talks with Doors about the need to go underground again. At a press conference, a Resistance member challenges new transformation group, which provokes one of them to fire a gun into the crowd. The Resistance grabs Pearl, and find that her brain scan reveals memory alternations but they need to prove that they have become Taelon supporters.

At the opening of a new Taelon portal station, a strange flash of energy radiates from Dr Jeffrey Whitfield, Director of Portal Research, and he collapses and found dead. Sa'al, the Taelon engineer in charge of the new portal, addresses the press about the safety of the portal. Doors argues with him and Sa'al explodes in a flash of light. Liam and Sandoval view video of both public events, they zero in on Arnold Creighton, a professor and outspoken critic of the Taelons. Augur finds that Creighton has invented a mini teleportation device, which can kill from the inside out.

While Chandler studies a stolen Taelon shuttle, two men burst in, and incinerate the lab while the shuttle escapes. Liam and Lili go the site and find evidence that the attack was an inside job, pointing to a Resistance traitor. During a gun battle at a warehouse, Lili finds Chandler, who asks her to join him and take arms against the Taelons. Lili promises nothing, and lets him escape. Liam and Lili discover that Chandler is planning an attack on the Taelon embassy in Washington.

A "volunteer" squad of specially trained Taelon implanted teen-agers attacks an abandoned warehouse where a Resistance cell meets. Lili, Liam and Augur are surprised when Julia shows up with an unconscious Amanda. Dr Park removes Amanda's implant and tells them that her implant is killing her. Resistance sends Julia undercover to join the Taelon Volunteer Program. Julia warns Liam and Lili about a massive assault, who mobilize the Resistance for a counter attack. Liam learns that recruits are being sent through portals after an unknown enemy in another galaxy.

Lili becomes infected by a highly addictive drug called Bliss. Liam and Sandoval go to Ireland to investigate the drug's origin, where they meet Dr Cox, and a cult of "Taelonists" who deny knowledge of Bliss. They discover a lab where Ma'el worked on an antidote for Bliss, suspecting the Taelonists found the lab and are spreading Bliss.

The Taelon's hire a spindoctor who brings on a reporter onto the mothership. Unfortunately the mothership is at this time hijacked by a replicant who wants to get the ship into Jaridian space.

Two unidentified Taelon piloted shuttles appear, unscheduled, in earth airspace, dogfighting. Liam wonders why Da'an took off to an unknown location. Sandoval is sent to locate the surviving Taelon, noted to be unco-operative. Zu'or disrupts Da'an's Karpag on the moon base home world recreation. Liam finds Ba'li, who claims to have come to help humans retake earth. Augur severs Ba'li's commonality link. Ba'li fingers Da'an as the architect of Taelon strategy across the galaxy to defeat the Jaridians. Ba'li turns into an Atavus and goes to kill Da'an.

After Augur's friend implodes, due to ID space inside him, Augur meets a beautiful woman, Beverly Wu, who hires him to engineer a weapon of mass destruction, called Forge in Antarctica. Zu'or tells Da'an that the latest battle with the Jaridians has ended badly and they are retreating. Zu'or wants to activate the Forge to strike at the Jaridians while they regroup. Da'an is against using Earth as a base for attacking, but Zo'or overrules him. Doors says Augur is in trouble if he's working with Beverly. Liam tries to get information on Forge from Da'an, who refuses to answer. Augur, falling in love, thinks the project may turn earth into a blackhole. The worm hole between earth and the Jaridian Empire stays open too long in-between firings.

A probe crashs on earth. The Resistance finds the probe, before Sandoval arrives, and takes it to a hideout. The hideout is ambushed and they are taken to a 'Dark Knight' base. The Resistance deals with this unexpected new player as they try to stop a Jaridian probe from an assault on Earth. The probe takes the shape of Augur, and delivers a message to humanity.

While Doors is holding a press conference, Liam sees a man videotape the room. When Liam confronts him, the man runs from the building. Both exchange gunfire, and the man turns his weapon on himself and is vaporized. Augur discovers the man had a Taelon warrior implant. Julia gets a tip of the implant and an arms dealer named Margolis. Julia and Augur questions Margolis about the deal with the warrior implant. They find the weapons are undetectable by security. One of the warriors bursts in and vaporizes Margolis. Julia and Augur can't seem to stop the warrior and finally escape by racing off in a car. Liam suspects the Resistance is being set up, and is reluctant to put members in danger at the next public debate. Julia secretly offers her unit's protection to Doors for the debate. Liam arrives at the debate and is furious to find Julia armed. Liam discovers three warriors, disabling two of them while a third escapes. Julia and her team respond to the alert and find they have been set up.