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.

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.

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.