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.

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

Boone encounters Julie, a suicidal young woman with artificial limbs as hands, who is being used by a religious leader as a miracle when her hands are regenerated by taelon technology.

Major McIntyre confronted Rho-ha in Johnson's hospital room, a struggle ensued and McIntyre was killed. Boone and Sandoval defend Rho-ha, who is ordered to stand trial facing the death penalty for murder. The prosecuting attorney is Joshua Doors, the estranged son of Jonathan Doors. Travis Perkins, delusional Taelon supporter, has vowed to kill those who pose a threat to Rho-ha. Joshua confronts Rho-ha on the stand about the DNA experiments, Rho-ha becomes enraged and threatens to kill Joshua. Perkins is angry at the treatment of the Taelon and attempts a suicide bombing.

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.

Boone and Lili investigate a small Amish town after several of its citizens mysteriously die.

Several soldiers who have volunteered to train in Taelon Interdimensional flight have instead been the victims of strange experiments - some have disappeared all together. A high ranking officer kidnaps Da'an in an attempt to have his men released.

Lili loads Augur's computer virus into the Taelon system and it takes affect immediately. System after system crashes and Lili and Da'an are in grave danger as the virus infiltrates the shuttle's computer and lurches them out of control. Augur thinks he can stop the virus, but he must send Boone deep into the building to access the central computer.

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.

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.

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.

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.

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

Liam is implanted with a neural surveillance device to track Da'an, who leaves earth on a mysterious final journey.

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.

The Taelons' fate - and possibly Liam's - is decided after Liam and Renee find Ma'el's regeneration chamber. The discovery of the secret location causes the surviving Taelons and Jaridians to seek the mechanism, which promises to restore their draining energy. Street, meanwhile, solves the riddle of Ma'el which will allow the Taelons and the Jaridians to join.

Boone investigates a serial killer programmed with a CVI who tried to kill Da'an when he enacted an ancient taelon myth of good conquering evil.

A construction blast unearths a grave marker belonging to a Taelon scout sent to size up earth for Companion occupation thousands of years ago. Boone must find the grave which contains the research, before Sandoval finds the grave. Da'an loses his position as the United Nations Companion to Zu'or, but keeps the American Companionship.

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.

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.

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.

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.

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.