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.

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.

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.

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.

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.

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.

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.

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.

Liam learns more about skrills while searching for the missing skrill queen.