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. Zo'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.
"They are the Companions. Aliens, come to earth on a mission of peace. Their true mission, the secrets they hide, forever alter humanity. In the struggle for our planet, the battle between these Taelon Companions and the Human Resistance, holds the key to Earths future and the fate of mankind. On EARTH: Final Conflict"
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 made synod leader by default.
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.
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. Zo'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.
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.
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.
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.
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.
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, discovered and taken hostage. Blanchard reveals to Lili that he is really her father, Colonel Purcell.
When a Taelon experiment to create an new hybrid warrior goes wrong, an ancient alien evil is unleashed upon the Earth.
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 looses his position as the United Nations Companion to Zo'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 Zo'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.
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 on 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 Augur 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.
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.
Sandoval's CVI is degenerating. 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.
The Skrills have been bioengineered on the Earth to be a weapon for the humans who assist the Companions. A Skrill from the first generation infests a bioengineer who goes underground, bent on freeing all Skrills from the oppression of the Companions.
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.
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 investigates a serial killer programmed with a CVI who tried to kill Da'an while enacting an ancient Taelon myth of good conquering evil.
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.
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