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