After Police Captain William Boone's wife is killed, he is recruited to work for the taelons, a seemingly benevolent alien race that has been on Earth for 3 years. To do so he will be implanted with a CVI- a cyber viral implant that will expand his mental abilities and allow him to control a bio-weapon of unlimited power. However before he can make his decision he is also recruited by the resistance, a group of humans who oppose the taelons being on Earth. Lead by Jonathan Doors, the resistance informs Boone that the taelons are not what they appear to be. The CVI implant brainwashes its subjects into following the taelon blindly, in effect controlling them. The resistance informs Boone that they can remove this aspect from the CVI on the condition that he works for both the taelons and the resistance. Boone accepts and now searches for the truth of why the taelons are on earth and if they are responsible for the death of his wife.
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.
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.
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.
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.
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.
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.
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.
Ne'eg dies from being exposed to a devastating virus that was unleashed from an alien probe. The virus falls into the hands of a group of white supremacists, they release the virus into the Lincoln Hills homeless shelter. The deadly virus quickly spreads, threatening to decimate both the human and Taelon races. Boone, infected with the virus, comes up with an idea to develop anti-bodies against the virus but it may not be in time to prevent the virus spreading over earth.
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.
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 minutes 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 set 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.
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.
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.
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.
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.
A Jaridian probe crashes into earth and disrupts the Commonality, leading the Taelons to round up suspected Resistance members to be harvested for their life force energy to feed the draining Commonality. As Augur, Maiya and the others lie near death, their souls are in a dream world. Liam, in a comatose state, finds them and tries to bring them back, but they are happy in their dreams and refuse to return. Lili and Sandoval locate the probe in Australia.
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.
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.
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.
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.
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.
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.
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.
A "volunteer" squad of specially trained Taelon implanted teen-agers attacks an abandoned warehouse where a Resistance cell meets. Lili, Liam and Augur are surprised when Julia shows up with an unconscious Amanda. Dr Park removes Amanda's implant and tells them that her implant is killing her. Resistance sends Julia undercover to join the Taelon Volunteer Program. Julia warns Liam and Lili about a massive assault, who mobilize the Resistance for a counter attack. Liam learns that recruits are being sent through portals after an unknown enemy in another galaxy.
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.
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.
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.
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.
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.
Da'an hires a professional hit man to seek out Augur. Liam and Renee meet with 10 Resistance leaders whose cells have been discovered and destroyed. In order to avoid one cell from crushing the entire network in the future, Liam proposes that he be the only communication link between cells. Sandoval learns that he will die unless he gets a blood transfusion from an immediate family relative.
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
The Companions are invited to join with a religious order in a ceremony. The group is made up entirely of women and seeks that special spiritual connection with the Taelons that will bring them to an enlightened state. Liam finds a former resistance member, Elizabeth, in the group. During the ceremony, the Companions share their energy with The Cloister. Worried about the possible security leak, Liam and Renee have to stop Elizabeth from telling the cult everything.
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.
At the Taelon Embassy, Da'an shows reporters the Taelon Galactic Database. A sniper fires a Pulse Gun that penetrates the virtual glass of the embassy. Liam and Da'an are stunned to see gaping holes in the virtual glass that is impervious to all human weapons. Sandoval and Liam find the Hammerlin CD-57 Pulse Gun and the transducer. Sandoval tells Liam he does not want the media informed. Later, Sandoval informs Zo'or that he has leaked all the information to the media, as per their plan. Augur identifies Scott Pierce from a webcam as the shooter, but discovers that Pierce is a patient at St John's Neurological Centre. On the Mothership, Zo'or transfers his energy into Pierce's comatose body to convince humans to ban energy weapons that could threaten the Taelons.
Liam is asked by a Church of the Companions member, Devon, to help find his girlfriend, also a member who has mysteriously disappeared. Sandoval gives Da'an some energy dust. Liam and Renee join the Church as homeless people. At the church's shelter they find that the food has a Taelon additive. In an underground environment on Church of the Companions land, Volunteers force drugged Church of the Companions members to harvest Kryss, a substance necessary that is vital to Taelons survival on Earth. Laim knows that Taelon plants only grow in 98F degree temporature. They discover that humans are being used to grow Kryss.
While Carson Briggs works overtime at the New World Commonwealth Bank, a hopeless cry introduces a blue light that swirls around him. The energy light chases and tortures Carson, pushing him onto the floor. The energy whirls in circular motions around Carson, setting him on fire. At the same time, Liam dreams of the exact horrifying events that Carson experiences. Liam goes to the death scene. Recalling the events of his dream to a investigater, he offers a piece of evidence that had not yet recovered - Carson's ring, which designed with the bank's logo and the ancient Taelon symbol for impurity. At Carson's home, Liam discovers circular burn marks throughout the house. The blue energy appears, which leads Liam to a Taelon datalog. The energy takes the shape of the deceased Taelon Ku'don, who mutters the word 'exile' before disappearing. Suddenly, Liam hears loud banging and he hides the datalog as commandos storm the house. Liam overpowers one of the commandos and escapes as a command
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.
Lili Marquette gives birth to a half jaridian child, with the help of taelon core energy, that may be the last hope for the taelon and jaridian race. Auger goes into hiding from volunteer investigations, an old friend of his J Street agrees to help Liam and Renee while Auger is on the run. Sandoval tries to destroy evidence of the Jaridian existence.
A party for the new elite is in full swing at pro-Taelon Senator Edward Gale's posh Washington home when his daughter, Eva appears with a gun. She fires, wounding him in the arm before his security guards can subdue her. The next day, Liam Kincaid and Renee Palmer meet with a holographic messenger sent by Hubble Urick. He informs them of the shooting and tells them Eva is in the hospital, having tested positive for Kryss, a substance used by Taelons in small quantities to help them adapt to Earth's atmosphere. Liam is surprised and angry, as the Taelons' Kryss facility was shut down eight months before and the Taelons swore they found a way to synthesize Kryss without enslaving humans. Yet Eva, whom the messenger tells them disappeared three weeks before to take part in an archeological dig, must have been enslaved in a Kryss factory to have traces of the substance in her bloodstream. Liam and Renee must prove the factory is still operating. When Liam visits Eva in the hospital, she te
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.
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 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.
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 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.
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.
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.