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.

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.

President Thompson declares a state of emergency to crush the resistance while Liam and Auger try to prove that the resistance was not behind the assasination attempt of President Thompson.

Liam and Augur discover that Volunteers all over the world are breaking into homes and arresting civillians. Meanwhile, Sandoval genetically alters Lili and sends her off into space.

Zo'or and Liam crash in a remote area of Wyoming. Naraina Durrant, a resident of a local commune of natural purists known as the Children of the Earth, rescues Liam from his crash bubble and assists him in his search for Zo'or. Meanwhile Zo'or's bitter rival T'than calles an emergency meeting to propose Da'an take Zo'or's place as the Synod leader.

Zo'or discuses with Ro'am, the Latin American Companion, his idea to make President Thompson an advisor to the Synod. Sandoval approaches Tonio Arias, Ro'am's Protector, and secretly attaches a microchip to Tonio's skrill. Ro'am and Tonio are killed while travelling in the ID Portal. T'than becomes suspicious of Zo'or because Ro'am's death shifts the balance of power in the Synod in Zo'or favour.

While Liam and Renee investigate the suspicions of false imprisonment and infringement of civil rights, an ammoralist associate of Augur's plans to steal Zo'or's gold onboard the mothership.

The ANA manages to negotiate amnesty for all resistance members, Liam trys to convince resistence member Halley Simmons to take up the offer. Sandoval uses parasites to make volunteers do suicide missions against the resistance

Renee discovers that her younger brother is a victim to Zo'or's plot to harness human emotions.

Liam and Renee investigate a serial killer who murders people in their dreams.

Liam and Renee discover that a baby is born with a CVI implant.

Zo'or threatens to attack the earth after an artifact containing the secret to synthesise taelon core energy is stolen from the mothership.

J Street learns a lesson in trust while on the run from Sandoval.

The fate of the earth and the taelons may be revealed when three astronauts from the future are discovered in stasis hidden in a government base.

In exchange for immunity, Sandoval agrees to testify against the taelons.

The Taelons' decision to enter death stasis causes a rift between Zu'or and Da'an, who refuses to share the core energy he has accumulated. Meanwhile, Liam learns that he only has days to live.

William Boone, the Taelon Protector who secretly led the human Resistance movement three years ago, is awoken from a state of suspended animation aboard the Mothership by Sandoval. He awakens to find that the Taelons and Jaridians have merged to become a new alien species posing an even greater threat to humanity and joins Renee's crusade against the Atavus.

Renee visits Boone and shows him a crystal that can project the location of every Atavan on Earth. In an effort to retrieve the crystal, Sandoval brings Zo'or back to life as an Atavus so that she can battle her old nemesis Boone.

Renee and boyfriend Captain Michaels "do-the-right-thing" as they risk their own personal integrity in an attempt to secure plans to the one military weapon that can kill the atavus.

Renee is put on trial for opening an Atavus stasis chamber.

Renee hooks up with Captain Michaels to investigate a pharmaceutical plant manufacturing an Atavus Hybrid vaccine. But something is a little strange about the lead scientist Dr Spangler. Ra'jel returns to lead Renee on an enlightening trip down memory lane. Why did the Taelons pick Earth? Things take a very deadly turn at the lab; Michaels is seriously injured, Dr Spangler's truth is revealed, and, as the Captain fights for his life, Renee must make an awful final choice.