Boone is caught in the middle of his double life when his old flame comes back in his life claiming to be working against the companions.

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

Oblivious to Boone and the resistance, Jonathan Doors comes out of hiding and launches a media campaign against the taelons, leaving Boone to clean up the mess.

At resistance headquarters, Boone meets two molecular biologists, Sahjit Jinnah and his fiancee Rayna Armitraj, who are studying the alien probe captured after it wreaked havoc in an Amish community. A power surge causes Rayna to cut off the top of the probe, which responds by dematerializing her. Unaware of the situation, Sahjit and Boone discuss with Doors and Auger the probe's purpose, recalling its ability to replicate butterflies into killers. Launching the resistance into battle with the probe that may be studying Earth.

At a Conference of Psychic Sciences, "The Commonality" the Taelon psychic link has been invaded and the secret plans for Earth are known. Katya Petrenko possesses incredible psychic gifts and an interest in Boone. She confronts Zu'or, telling him that the Taelons must change their approach to humans, or they will destroy both races. Katya reveals that a taelon named Ma'el gave some humans the gift to break into "The Commonality". As Katya dies, Dr. Belman performs a brain transfer of all of Katya's knowledge to Boone.

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.

Divers stumble across a strange radiant canister while searching for sunken treasure. Upon opening the canister an alien being known as Ha'gel is released from its prison and assumes the identity of one of the crew and destroys the others. Boone is called to the crime scene and his suspicions are raised when he finds Taelon writing on the empty canister. Upon questioning, the Taelons tell Boone that Ha'gel is the last of an alien criminal caste. Afraid that Earth will learn the truth, the Companion's recruit the help of Beckett to deal with Ha'gel. Ha'gel assumes Sandoval's form, and confronts Beckett.

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 hours 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 sent 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.

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.

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.

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.

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.

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.

Juda's death spells hope for Renee in her battle against the Atavus.

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.

As Renee begins to lose hope that humanity will survive, an old friend reappears to give her guidance and solace. Yulyn and Ra'jel will join forces to deliver the final blow to the atavus threat to mankind. Sandoval comes to term with his past, and ends the series in a very fitting "Sandoval" manner.