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.

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.

Nine hours after Beckett conceived, her child is born. The Resistance must decide what to do with Beckett and her rapidly developing child, Liam Kincaid, who reaches maturity within hours of being born. Sandoval reveals Boone's ultimate fate to Lili. Rayna transmits a signal to the Jaridians, an alien race. A Jaridian probe replicant assassin is sent to destroy all Companions. At Boone's funeral the Taelon Synod leader, Quo'on, is assassinated, but Liam saves Da'an. Da'an appoints Liam as his personal protector. Zo'or realizes that if the replicant kills Da'an, then he'll be made synod leader by default.

After Augur's friend implodes, due to ID space inside him, Augur meets a beautiful woman, Beverly Wu, who hires him to engineer a weapon of mass destruction, called Forge in Antarctica. Zu'or tells Da'an that the latest battle with the Jaridians has ended badly and they are retreating. Zu'or wants to activate the Forge to strike at the Jaridians while they regroup. Da'an is against using Earth as a base for attacking, but Zo'or overrules him. Doors says Augur is in trouble if he's working with Beverly. Liam tries to get information on Forge from Da'an, who refuses to answer. Augur, falling in love, thinks the project may turn earth into a blackhole. The worm hole between earth and the Jaridian Empire stays open too long in-between firings.

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.

At One Taelon Avenue, Dr Sato and Joshua Doors begin a test with an ID shuttle prototype. The craft explodes, sending everyone ducking for cover while Sato calmly watches. Joshua tries to persuade Renee Palmer to leave Doors International and join him at One Taelon Ave. Jonathan Doors encounters his son in Renee's office and the two exchange opinions about business. Jonathan, concerned about his son, asks Liam to find out what's really going on at One Taelon Ave. At One Taelon Ave, Renee meets with Joshua while Liam is tracked by Control, a computer, while he investigates. Control tracks Sato and begins a bio-purge function. Sato tries to escape the energy walls, but they disintegrate him. Zu'or and Da'an review the security video of Sato's demise. Da'an is concerned that Control may be overriding the Taelon programming and creating its own agenda. Sandoval reports he has begun an investigation at One Taelon Avenue, but Zu'or orders him to close his investigation. Liam and Augur find t

The Murder of General T'Than on board the mothership leads Liam to descover the taelons darkest secret, while the late Jonathan Doors rturns in cyber form to addminister a deadly attack upon them.