Lili is taken hostage as a Jaridian escapes from the Taelons in a shuttle. Liam pursues and both shuttles are drawn into a alien vessel. Liam explains that the vessel is a repository for the Kimera's accumulated knowledge. In order to leave, they must go to the vessel's core. Da'an confronts Zo'or about the Jaridian's escape, and challenges his authority. The Jaridian reveals his race and the Taelons were one until the Taelons separated. Now the Taelons want to force a union with the Jaridians by using humans as soldiers against them.

The mothership is damaged when a peice of dark matter colides with it.

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.

The Taelons' fate - and possibly Liam's - is decided after Liam and Renee find Ma'el's regeneration chamber. The discovery of the secret location causes the surviving Taelons and Jaridians to seek the mechanism, which promises to restore their draining energy. Street, meanwhile, solves the riddle of Ma'el which will allow the Taelons and the Jaridians to join.

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.

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.

The Companions are invited to join with a religious order in a ceremony. The group is made up entirely of women and seeks that special spiritual connection with the Taelons that will bring them to an enlightened state. Liam finds a former resistance member, Elizabeth, in the group. During the ceremony, the Companions share their energy with The Cloister. Worried about the possible security leak, Liam and Renee have to stop Elizabeth from telling the cult everything.

The Taelons' decision to enter death stasis causes a rift between Zu'or and Da'an, who refuses to share the core energy he has accumulated. Meanwhile, Liam learns that he only has days to live.

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.

Maiya begins to suffer from dimensional phasing, Augur claims that Maiya and her counterpart Isabel must merge or they may both die. Doors enters presidential race to begin to challenge the Taelons. Lili confirms that Isabel and her have the same father. Sandoval questions Maiya on the mothership, while Doors and Zo'or discuss joining forces.

A probe crashs on earth. The Resistance finds the probe, before Sandoval arrives, and takes it to a hideout. The hideout is ambushed and they are taken to a 'Dark Knight' base. The Resistance deals with this unexpected new player as they try to stop a Jaridian probe from an assault on Earth. The probe takes the shape of Augur, and delivers a message to humanity.

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.

President Thompson declares a state of emergency to crush the resistance while Liam and Auger try to prove that the resistance was not behind the assasination attempt of President Thompson.

The Taelons decide to leave earth following what appears to be an imminent Jaridian invasion.

The fate of the earth and the taelons may be revealed when three astronauts from the future are discovered in stasis hidden in a government base.

When Lili's shuttle is stolen by a friend whose mission to Mars was cancelled, Boone, without breaking orders to find the shuttle for the taelons, has to help the resistance make the most of the stolen shuttle.

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.

Augur is arrested for treason in Russia and condemned to death by hanging. However, he is blackmailed into participating in a Taelon experiment as advanced warriors and is implanted with a CVI. Maiya confuses Sandoval for her lover, Jason, from her dimension thus attracting Sandoval. For protection, Maiya takes the identity of Isabel Martinez. Liam helps Augur break his CVI and bring him back from the rage. Lazarus, the overseer of the program, was brought back to normal by Da'an.

With Da'an's help, a handicapped scientist genius, Sparrow, heads a program where disabled persons can transfer their consciousness into a healthy body by creating a biosurrogate with Jaridian replicant programming, and then live normal lives. A reporter sneaks into the lab and his camera flash activates a biosurrogate. Sandoval arrives to find the reporter and a guard dead, and the biosurrogate gone having no consciousness of it's own. Lili finds that Zu'or has tampered with Da'an's research and have programmed the biosurrogates into killing machines. Liam learns that Sparrow has transferred his consciousness into a second biosurrogate.

Two unidentified Taelon piloted shuttles appear, unscheduled, in earth airspace, dogfighting. Liam wonders why Da'an took off to an unknown location. Sandoval is sent to locate the surviving Taelon, noted to be unco-operative. Zu'or disrupts Da'an's Karpag on the moon base home world recreation. Liam finds Ba'li, who claims to have come to help humans retake earth. Augur severs Ba'li's commonality link. Ba'li fingers Da'an as the architect of Taelon strategy across the galaxy to defeat the Jaridians. Ba'li turns into an Atavus and goes to kill Da'an.

A Roman citizen is awoken uboard Ma'el's ship to pronounce jugement against the taelons.

While onboard the taelon mothership, Renee is taken hostage by a mysterious being that haunts the lower parts of ship.

Zo'or threatens to attack the earth after an artifact containing the secret to synthesise taelon core energy is stolen from the mothership.

J Street learns a lesson in trust while on the run from Sandoval.

After a Jaridian energy beam turns several Taelon companion protectors into assassins, Zo'or demands that they be turned over to him in 24 hours - or he will open fire on Earth. Da'an, meanwhile, dispatches Liam to take the assailants alive; and Sandoval becomes a pawn of the Jaridians.