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 learns more about skrills while searching for the missing skrill queen.

Liam and Renee investigate taelon artefacts on of which leads to the discovery of Ma'el's ship.

A woman barely escapes from the small town of Taelonville, Indiana through an ID Portal, the woman's three-month-old fetus was removed, possibly by ID technology. Zo'or denies the use of ID technology to perform non-invasive surgery. Liam arrives in Taelonville to investigate.

Lili awakens as a beam locks on to the shuttle. A Jaridian enters the shuttle as a Taelon warship arrives, engaging the shuttle in battle. Later, Lili finds herself to be a patient at a military hospital. Dr Reed tells Lili that she has been in a coma and that her CVI has been removed. Liam arrives to tell Lili that she has lost 3 years of her life and that the Taelons are gone after the Jaridians defeated them. She also learns she is responsible for saving Earth and Sandoval is scheduled to be executed. After Colonel Bramson debriefed her, Lili learns that Sandoval's last request is to speak with her. She agrees when she realizes that this will be her only chance to find out why Sandoval sent her out on the shuttle. However, Sandoval only reveals to Lili that he now has his own resistance, made up of faithful Taelon followers, who will kill her. Meeting Augur, Lili finds out that he is the CEO of a large company with a wife and a child. Watching Lili and Augur, Dr Reed and Bramson dis

A Roman citizen is awoken uboard Ma'el's ship to pronounce jugement against the taelons.

At One Taelon Avenue, Dr Sato and Joshua Doors begin a test with an ID shuttle prototype. The craft explodes, sending everyone ducking for cover while Sato calmly watches. Joshua tries to persuade Renee Palmer to leave Doors International and join him at One Taelon Ave. Jonathan Doors encounters his son in Renee's office and the two exchange opinions about business. Jonathan, concerned about his son, asks Liam to find out what's really going on at One Taelon Ave. At One Taelon Ave, Renee meets with Joshua while Liam is tracked by Control, a computer, while he investigates. Control tracks Sato and begins a bio-purge function. Sato tries to escape the energy walls, but they disintegrate him. Zu'or and Da'an review the security video of Sato's demise. Da'an is concerned that Control may be overriding the Taelon programming and creating its own agenda. Sandoval reports he has begun an investigation at One Taelon Avenue, but Zu'or orders him to close his investigation. Liam and Augur find t

Da'an checks with Andrea Myzar on the decoding process of one of Ma'el's messages. Da'an is shot by Andrea. Andrea leaves the MotherShip with Ma'el's message relic. Augur's holo-computer finds that Andrea is Emma King, a mathematican killed 3 years ago. Liam retrieves the relic and discovers that humanity is the genetic link between the Taelons and Jaridians.

While Lili returns to earth after being tricked into giving the jaridians interdimensional transportation, an auction is held at the Antartic Republic of Rostok for some mysterious alien weapons. Sandoval must stop the bidding taking place while Liam and Renee try to find out what the weapons are.

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.