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.

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.

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.

Sandoval's CVI is degenerating. While Dr Belman works to restore his CVI and save his life, Sandoval, free from his CVI, escapes to reunite with his wife, only to put her life in danger. Boone learns that Sandoval's CVI contained information about the Taelon's mission on earth, and tries to save Sandoval's life.

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.

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.

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.

When a taelon experiment to create an new hybrid warrior goes wrong, an ancient alien evil is unleashed upon the Earth.

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

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.

When Lili's shuttle is stolen by a friend whose mission to Mars was cancelled, Boone, without breaking orders to find the shuttle for the taelons, has to help the resistance make the most of the stolen shuttle.

The Taelons introduce interdimensional travel to human customers. A young deaf-mute boy and his mother become separated during their travels through the portal. The boy appears and is now able to speak and hear. The boy is examined by Dr. Park, a resistance doctor, who discovers that he has been implanted with a device to restore his missing senses. Boone suspects that the Taelons are using the portal to perform experiments on humans. Doors sends Sahjit through the portal with a tracking device.

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.

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.

Colonel Purcell and agent Carter discuss if the body of Thomas Blanchard, a thief who was beaten brain dead, is suitable for them. Doors International head, Anne Portnoy, demonstrates a new Taelon device, an EMP (ElectroMagnetic Pulse) weapon. Boone meets with Doors and Augur to warn them of the EMP. They plot to steal the weapon to prevent the Taelons from using it against Earth. Before they can obtain the EMP, Blanchard steals it. Lili sneaks into Blanchard's hideout, but is discovered and taken hostage. Blanchard reveals to Lili that he is really her father, Colonel Purcell.

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.

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.

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.

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.

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.

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.

A holographic image of Rayna, who was consumed by an alien probe, tells Augur that the Taelons are dismantling the probe which will kill her, and they will learn about the Resistance's secrets. Hearing of Rayna's appearance, Sahjit is determined to bring her back. The Taelon lab is under intense security and Augur hires a special operative, Michael Sloane, to lead the resistance team to infiltrate the Taelon compound to destroy the alien probe.

The mothership is damaged when a peice of dark matter colides with it.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

The joining of the Taelons and the Jaridians create the Avatus race, a greater threat that Renee leads the fight against.

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

After he sets up an Atavus fan Web site, a disaffected teenager is used by the Atavus to recruit the world's youth into its army of hybrids.

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.

Renee fights to destroy the Atavus as they begin a joining process that will create human-Atavan hybrids.

Sandoval strikes a deal with the Atavus while Renee tries to convince Hubble Urick about the existence the aliens.

Renee, with a former reporter, tries to inform the media about 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.

Renee suffers an emotional breakdown after a high-rise attempt to rescue a woman and her baby from an atavus attack goes horribly wrong. Unable to shake the image of the crying baby falling to its death, Renee and Street check into a spa to try to relax. Her therapy is soon cut short as they find themselves being stalked by Howlyn.

Renee breaks out a serial killer from prison, hoping she will be able to provide the information necessary to kill the deadly Atavus aliens, but the plan backfires.

A young woman, J Street, finds herself attracted to a seductive Atavus.

Renee receives part of an old manuscript from an associate of her Harvard professor, who believed that ancient Egyptians were visited by aliens. He claims he has discovered proof of this and then disappears. Renee visits the Giza plateau and fins she must hook up with an old flame, in fact her love, Raleigh Sinclair, who's a dashing British scoundrel and a rogue archeologist. The two must work together to search the Pyramids to locate the tomb of Askenaton, a Grand Vizier to the Pharaohs and possible ancient Atavus who had mystical powers. Renee and Raleigh have some good hot-tempered banter as they try to outwit each other, while Sandoval arrives to complicate things further.

This pivotal episode brings Renee Palmer to a hybrid-infested hospital where comatose patients are being used as a food source for the Atavus. It is only when Renee is ultimately able to expose these atrocities that the FBI finally takes seriously the threat of the Atavus, who must feed on the life force of humans in order to survive. The FBI pledges to join Renee's crusade to destroy this formidable alien menace before they take over the world.

Renee attempts to sabotage Sandoval and Howlyn's plans for producing Atavus regeneration chambers.

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.

J Street has become an Atavus hybrid, Renee rushes to locate an antidote.

Renee has a change of heart and sympathy for her unwilling enemy as she becomes aware of the inhumane treatment the atavus hybrids must endure in government run internment camps.

Renee's personal image of mankind's greatest enemy is forever changed when she becomes emotionally involved with a young atavus child, Yulyn, whom reveals he has a very human-like soul. Renee must now protect Yulyn, also a royal, from Howlyn's evil clutches.

Renee travels back through time in pursuit of a deadly female 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.

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.

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

Renee is torn between love and duty when her boyfriend is captured by the Taelons.

A reporter after being exposed to Taelon radiation seeks to expose the Taelons during a live television interview with Zo'or by airing secret Taelon video.

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.

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

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

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

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.

Liam investigates if Jack Patches, that allow fans of the combat game Pa'dar to feel the feelings of the warriors, causes seizures.

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

When Zo'or contracts an ancient deadly plague for which there is no known cure, Renee suggests to Liam that the virus could be used to create a biological weapon to fight the Taelons. She recruits Augur to research the virus and it's potential.

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.