Picking up in the train yard, Henry meets with who he thinks is an FBI agent. However, when he admits that Edward works for Janus, the agent pulls out a gun to shoot him. Before he can, Norah Skinner shoots the agent, saving Henry. Norah explains that Proctor wasn't an FBI agent, he was a "watcher"; part of the System Management group that Norah leads. System Management is Janus' internal police force.
Norah needs help disposing of Proctor's body, worried that no watcher has ever gone missing and Trumbull will be suspicious. Norah tells him that she is the only person he can trust. Edward wakes up at Henry's and heads into the kitchen, where he sees Angie.
Angie lets Henry (actually Edward) know that Mary thinks Tom is having an affair and has hired a private investigator to follow him. He immediately alerts Mavis of this development. When he calls in, Mavis tells Edward that Raymond is missing; he hasn't returned.
Edward enters into Henry's world at AJ Sun. Ellen Freeh, a fellow consultant, approaches him. She's worried that she is going to get fired. Arlene interrupts and lets him know he's need downstairs. There is he is met by Norah and Trumbull, who put him through a lie detector test to prove his loyalty and that he's not broken.
Norah beams a light into his eyes, transferring questions he is to answer rather than answering those she's asking in person in order to pass the test. He passes. Trumbull, Mavis and Edward discuss Raymond's disappearance. Trumbull agrees to go into the field with another operative. Ellen Freeh, operative name Paula, is chosen to go with him.
Raymond was captured in Russia; Paula and Edward travel to rescue him. While Paula distracts the guards, Edward makes his move. Edward finds Raymond, rescues him and gets him to the guard station.
There, a gunfight ensues. Edward turns to Henry and can't fight back. Paula gets shot. Henry calls in and accidentally reports to Mavis as "Henry Spivey." Paula hears him. So does Raymond, who rushes to get them into the car and leave.
Back at Janus, Mavis is concerned that Paula may have heard Henry call in. He doesn't want Edward to know about Paula, worried that he will kill her to protect himself. Mavis lets them know that Trumbull is more suspicious than ever. Mavis tells Henry to go to the hospital to meet with Paula's husband, who thinks that she and Henry were carjacked.
Before heading home, Tony has Raymond meet a woman at a restaurant providing an opportunity for the Private Investigator to snap photos of him to give to Mary. They have to make an affair look real since Raymond was captured for several days and wasn't able to make contact.
Henry visits Paula at the hospital. There he sees the guards that Mavis has sent to watch Paula's room. Back at home, Henry listens to Edward's message. Edward says that Jack is lying about taking guitar lessons. He suggests that Jack might actually have some his side of the gene pool.
Edward pays Dr. Skinner a visit at AJ Sun. She lets him know that Paula may have heard Henry break cover, but they won't know until she wakes from her coma. Edward and Norah share a passionate kiss, revealing that they have a secret relationship. The next morning, Henry wakes up in a hotel room while a woman showers. He grabs his clothes and leaves, not realizing its Norah.
Back at home, Henry walks in to see Angie and Jack. He is upset and struggling with the fact that he just left the bed of another woman. Henry confronts Jack about lying about taking guitar lessons. Jack tells them to meet him later that night to see what he has been doing.
Mary confronts Tom at the office about the affair. She has photos of him with the other woman. Henry sees Mary just as she's leaving the AJ Sun office. He knows what has happened. Henry goes to Dr. Skinner to follow up on the latest mission. He questions how she lives with herself with all she does. Without knowing that Edward and Norah have a relationship, Henry calls Edward a whore and that sleeps with several women night after night.
Angie and Henry go to the location Jack suggested. There, they see Jack participate in a form of fighting combat. Jack shows great movement and ability to fight, which concerns Henry. Angie videotapes the fight. Henry has to walk out. Although it's an aggressive form of fighting, Angie is just glad her son isn't doing drugs.
Tom and Mary meet with Dr. Skinner to talk through the affair. Norah encourages them to earn each other's trust back. Norah pushes Mary to promise she'll drop the private investigator.
Tony lets Norah, Mavis and Trumbull know that Paula is waking up from her coma. Henry gets there first, unaware of this. When he doesn't see anyone, he's worried that Edward got to her. Back at Janus, Tony switches Tom to Raymond and lets him know that Edward needs a favor. Henry catches Tom getting off the elevator. But, he realizes its Raymond, not Tom, and tells him he already took care of Paula, which convinces Tom that he's Edward.
Just as Henry and Raymond leave, Norah and Trumbull pay Ellen a visit. Tony alerts Norah that he is going to remote switch Ellen to Paula. She tells them that she heard Edward call into Janus using the name Henry Spivey. Trumbull has asked them to put termination orders into effect. Norah gathers the mission files. Norah goes to visit Paula to switch her back to Ellen, while she uploads memories.
Trumbull pulls Edward in to let him know that since he's broken, he will be terminated and he will live only as Henry. Just before they take him away, Ellen enters with a gun.
Norah implants memories into Ellen's mind about Paula's missions to make her appear broken. All to save Edward.
Paula is now just Ellen! Ellen retires from AJ Sun.