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Jarod has been caged like an animal at The Centre since his capture on the tarmac, and Lyle tries every tactic he knows to brainwash him.

In preparation for returning him to the Triumvirate and Mutumbo in Africa, Lyle thinks he has sedated Jarod, but Jarod manages to avoid taking the drugs. While waiting for an opportunity to escape, Jarod learns about "Project Silence," a Centre-sponsored hit on the Nash family run by a covert team assigned to Lyle by Mutumbo. Jarod sees his chance to get away and overpowers both Sam and a mysterious man whose name is Mr. White to escape from the plane.

Dr. Jarod Hickum, part of the team that designed the Cassini Probe for NASA, sets out to expose "Project Silence" and save the Nash family and everyone else whose life will be endangered by it. He quickly realizes, however, that the secret of "Project Silence" can only be found at the Department of Energy.

As Jarod "Watts," the Pretender becomes a D.O.E. Agent. He discovers that Clare and Jason Nash realized that someone was attempting to use their propulsion research for weapons applications and tried to "blow the whistle." They were prevented from doing that when an attempt was made on their lives. This resulted in the family becoming separated as part of a witness protection transfer program. Jason Nash refuses to testify until his family is together again, which will take place at the atomic research lab. Jarod gets assigned to Agent Timson's team-the one protecting Clare Nash until she can be reunited with her husband and daughter, who are being held at another location.

Except for a brief visit to Miss Parker while she is in the hospital, Mr. Parker has gone into hiding while he devises a way to regain control of The Centre. His mental state is uncertain. He recites a quote from Shaw to Miss Parker, saying that a family is a tyranny ruled over by its weakest member. He later tells her (via a phone message) to catch Jarod at all costs, because he's the key, "the only key."

Miss Parker challenges Mr. Raines, intending to shoot him for the bullet she took for her father-the one that Raines ordered Willie to shoot. But Mr. Raines reappears to have found God during his absence. Shaken by his newfound faith and his willingness to let her shoot him for his past sins, Miss Parker relents and lets him go.

Angelo e-mails Jarod with information that identifies D.O.E. Agent Timson as the traitor who is really a part of "Project Silence." Jarod realizes that "Project Silence" has been designed to keep the Nash family from testifying by blowing up the building in which they are to be brought together again-the atomic research lab.

Jarod locates Mr. White just as he has finished planting C-4 on a 10-minute timer in the hazardous-materials section of the building. Mr. White insures his own escape by tossing pictures of Jarod's sister and family, which may have current addresses on the back, into a lit furnace. Jarod rushes over to pull them out and manages to save most of them, but Mr. White escapes as planned.

Agent Timson delivers Clare Nash to the facility and, unaware that Jarod has disarmed the C-4, fakes a reason to leave five minutes before he thinks the bomb is going to go off. Jarod prevents his departure and turns him over to Agent Blaine, who is not on The Centre's payroll. Jarod reunites the Nash family, giving them a packet with the information they need for their new life and promising them they will be safe.

By the time Miss Parker gets upstairs, Jarod is gone, but he has left her a little box of "goodies," enough for her to realize that there was a bomb in the building that should have gone off while she was in it. This means that the only person Mr. Parker has told his daughter she can trust is the brother who first had her committed to a hospital, and then tried to have her killed by sending her into a building he thought was going to be blown to smithereens.

Afterwards, Lyle covers his surprise at seeing Miss Parker alive by attempting to lay the blame for Jarod's escape at her feet. She refuses all responsibility and gives him the box that Jarod left for him in the building. It contains the cables that Lyle used in his attempts to torture and brainwash Jarod. The cables have a note on them that says, "See you soon, J."

Later that night, Jarod looks for his sister, Emily, using the address he found on one of the pictures that he was able to pull out of the furnace. He finds that he has just missed her-she is gone. Forlorn, he calls Miss Parker. She says that maybe the world really is changing. Jarod says it doesn't matter how much it changes, because they are both still alone in it.