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 attempts to track his wife's murderer. He is determined to find out if it was the taelon companion Da'an who ordered her death to get Boone to work for the companions or if it was the resistance that killed her, securing Boone as the resistance's eyes and ears of the companions.

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.

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.

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.