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.

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.

Zu'or sponsors a "fountain of youth" program, called Second Chances, which makes old and ailing people young again. The resistance are trying to replace Doors as leader. Pearl Bell says that she had no previous use for the Taelons before she undergoes the first public transformation. While being interviewed afterward she states how Taelons had before helped her son live. Resistance talks with Doors about the need to go underground again. At a press conference, a Resistance member challenges new transformation group, which provokes one of them to fire a gun into the crowd. The Resistance grabs Pearl, and find that her brain scan reveals memory alternations but they need to prove that they have become Taelon supporters.

At the opening of a new Taelon portal station, a strange flash of energy radiates from Dr Jeffrey Whitfield, Director of Portal Research, and he collapses and found dead. Sa'al, the Taelon engineer in charge of the new portal, addresses the press about the safety of the portal. Doors argues with him and Sa'al explodes in a flash of light. Liam and Sandoval view video of both public events, they zero in on Arnold Creighton, a professor and outspoken critic of the Taelons. Augur finds that Creighton has invented a mini teleportation device, which can kill from the inside out.

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.

Liam and Augur discover that Volunteers all over the world are breaking into homes and arresting civillians. Meanwhile, Sandoval genetically alters Lili and sends her off into space.

Lili awakens as a beam locks on to the shuttle. A Jaridian enters the shuttle as a Taelon warship arrives, engaging the shuttle in battle. Later, Lili finds herself to be a patient at a military hospital. Dr Reed tells Lili that she has been in a coma and that her CVI has been removed. Liam arrives to tell Lili that she has lost 3 years of her life and that the Taelons are gone after the Jaridians defeated them. She also learns she is responsible for saving Earth and Sandoval is scheduled to be executed. After Colonel Bramson debriefed her, Lili learns that Sandoval's last request is to speak with her. She agrees when she realizes that this will be her only chance to find out why Sandoval sent her out on the shuttle. However, Sandoval only reveals to Lili that he now has his own resistance, made up of faithful Taelon followers, who will kill her. Meeting Augur, Lili finds out that he is the CEO of a large company with a wife and a child. Watching Lili and Augur, Dr Reed and Bramson dis