En este primer episodio, se presenta la figura del capitán de policía William Boone, cuya mujer ha sido asesinada. Después del suceso, es reclutado por los taelons, una raza extraterrestre benevolente en apariencia que está habitando en la Tierra desde hace tres años. Para hacer bien su trabajo, a Boone le implantan un dispositivo en el cerebro que expande sus habilidades mentales y le permite controlar una arma biológica de poder ilimitado.

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 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.

William ha vuelto a ver a Elise, una antigua amiga de la que estuvo muy enamorado. Elise va a quedarse en la ciudad como profesora de música y William quisiera comenzar una nueva relación con ella. No es su única preocupación: han robado un importante cargamento de material radioactivo.

Boone and Lili investigate a small Amish town after several of its citizens mysteriously die.

A punto de comenzar la final del campeonato de fútbol, con más de cuatro mil millones de personas delante de los televisores, se interrumpe la retransmisión y aparece en imagen un científico al que todos suponian muerto.

A punto de despegar hacia Marte una nave tripulada, el Presidente cancela la misión. Los extraterrestres han ofrecido colaborar en un programa conjunto que permita viajar a otras galaxias.

The "Skrills" have been bio-engineered on the Earth to be a weapon for the humans who assist the Companions. A "skrill" from the first generation infests a bio-engineer who goes underground, bent on freeing all "skrills" from the oppression of the Companions.

Durante un acto oficial en el Planetario, los asistentes han sido paralizados por un gas. Cuando William y sus compañeros de Seguridad se recuperan, el lider de los extraterrestres ha desaparecido.

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 in 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 Auger 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.

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.

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 loses his position as the United Nations Companion to Zu'or, but keeps the American Companionship.

William ha visto a Johnson, pero éste es un soldado que, al parecer, murió cuando secuestraron al jefe de los extraterrestres. Aunque quieren convencerle de que fue una simple alucinación, William cree que Johnson está vivo y trata de comunicarse con él.

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.

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.

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, but is discovered and taken hostage. Blanchard reveals to Lili that he is really her father, Colonel Purcell.

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.

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.

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.

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.

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.