Rosen tells Bill that they Cameron and Nina have captured a possible Red Flag suspect. They go to a concealed containment chamber that the DoD that has installed to contain captive Alphas. They talk about the fact that Bill still hasn’t regained his abilities, and Rosen worries that Bill may be dismissed by the team since he no longer has his abilities. Gary comes in and complains that the containment chamber wasn’t built to his specifications, and wonders why Bill is there.
Rachel calls and reports that Cameron and Nina are coming up with their prisoner, an unconscious Dr. Kern. They bring him in and Nina explains that her ability didn’t work on him. As they take him to the holding cell, the elevator door closes partway and then opens again. Rosen hears it but turns and sees nothing.
As Rosen puts Kern in the MRI chamber, Bill insists that he doesn’t need his powers to be useful, but Rosen says that they need him. Meanwhile, Nina fills out a report and Cameron gets her coffee. She notes that Kern is an obstetrician and must have recognized that they weren’t the happy couple they pretended to be. When Nina says that she discussed their relationship with Rosen and he doesn’t feel that it’s professional, Cameron says that they do unprofessional things all the time. Nina admits that every relationship she’s had was screwed up and Cameron reluctantly agrees. Bill calls them to meeting and once they’re gone, Nina’s laptop computer activates, seemingly on its own.
Rosen reveals that Kern has no optic nerves, which is why Nina couldn’t push him. Cameron points out that he functioned normally despite supposedly being blind. Meanwhile, Gary realizes that his phone was misplaced. Rachel finds it and Gary points out that the data files on it are opened. Rosen informs them that the DoD believes that Kern was doing Alpha research and splits up the team to go over the evidence from Kern’s office.
In his cell, Kern wakes up.
Rachel goes over urine samples in her office and catches a glimpse of someone moving with her enhanced senses. She steps out into the hallway to see who is there and hears a heartbeat from someone she can’t see. Gary interrupts her and Rachel asks if he was near her office. He says that she’s not making sense and goes back to his office. As Rachel walks away, something scratches the window glass behind her.
Bill and Rosen go into the chamber to see Kern. They ungag him and Kern demands his lawyer. Rosen informs him that he’s being held for involvement with a terrorist group and Kern feigns ignorance. Bill handcuffs him and stands him up against the glass, and Rosen throws a glass. Kern reacts and Rosen explains that he has the ability to “see” via sonar. Kern warns that it won’t end well and smiles.
Back in his office, Bill calls Clay and confirms he’ll be there in two hours to pick up Kern. For a moment he seems to hear something in his office but dismisses it as his imagination.
Cameron goes to see Rosen and asks for a little space so he and Nina can figure things out on their own. Rosen says that he can’t do it and Cameron starts to object, but Rachel comes in and says that she’s found something. She shows them vitamins for pregnant women, but when she analyzed them she found active human DNA inside of them. Rosen realizes that it could cause birth defects and mutations. Rachel hesitates and then says that she smells blood in the hallway. They go out and discover that Nina is having a nosebleed for no apparent reason.
Rosen goes to see Kern, who does an ultrasound of his chest and diagnoses him with a heart problem. Kern says that he took an oath to do no harm and Rosen asks why he’s giving active DNA to pregnant women. The obstetrician insists that he’s looking toward the future and reminds Rosen of the drug that can prevent the birth of Alphas. Kern explains that his drug is a counteragent and asks if any of Rosen’s team can read minds. When Rosen refuses to answer, Kern says that he’ll just have to wonder and predicts that men with guns will take him away. He warns that it’s a mistake and insists that the people who tried to kill Rosen were a fringe element of the Red Flag. Rosen doesn’t believe it, and Kern responds by noting that he wants the same future as Rosen, one where humans and Alphas work together. He believes that one day the unenhanced will be able to join the Alpha cause. Rosen offers to intervene on his behalf in return for information but Kern refuses and says that they’re at an impasse. When Rosen says he’s going to Binghamton, Kern asks why Rosen thinks that.
Rachel is working in her office when she hears a metallic clicking noise. She steps out into the hallway and tries to identify the source of the noise. Concentrating, Rachel hears the same heartbeat from before and boosts her eyesight to see compressed fibers in the nearby carpet. The elevator door opens and Rachel steps inside, and something grabs her.
Bill and Cameron consider how to break Kern and hear the computers activate on their own. They discover that they’ve been locked out of the system, which is running a keyboard retrieval program. Nina comes in and reports that Rachel is gone. They call out to her and get no response, and Gary discovers that there is a glitch in the digital recordings. He confirms that Rachel entered the elevator 20 minutes ago and the team goes to find her. They find blood and drag marks on the carpet and Cameron notices a crack in the ceiling.
Rosen goes to see Kern and asks what he’s done to Rachel. Kern insists that he hasn’t done anything and that he’s chained to a table. He tells Rosen that the number of heartbeats in the building haven’t changed and there have always been eight people in the building. Rosen points out that there are only seven people in the building, much to Kern’s surprise. He asks if things have gone missing around the office and there have been strange sounds. When he realizes that has happened, Kern tells Rosen that they have an unexpected guest and if they don’t release him, things will get worse.
Rachel is tied up and gagged and left unconscious in an air vent.
Kern yells at the cameras, demanding that they release him. Rosen suggests that they consider what Kern is saying. When Bill notes that he had a sense that someone was there, Rosen explains that it’s a matter of perception and demonstrates that people have a blind spot wired into their brains. He believes they are dealing with an Alpha who can exploit that phenomena. When Nina wonders how the Alpha can avoid the cameras, Gary points out that the internal cameras are glitch but that there is a camera in the next building. He tunes into it and brings it up on the monitor, and they see a woman in the room with them. Cameron tries to attack her but she cuts him with a knife and slips away, activating the blast door and sealing them in.
They confirm that their attacker has changed the passwords and locked them out of the system. They need Gary to override the system, but he’s busy panicking and throwing chairs at the windows until Rosen calms him down.
Nina treats Cameron’s wound and offers him painkillers, but he points out that he’s an addict. They grow closer even though they both admit they’re bad for each other.
Bill discovers that his gun is gone. They hear gunshots and run to the containment chamber. Their attacker has tried to shoot through the window without success. By the time they get there, she’s gone. Kern explains that the stalker is named Griffin and is considered an unstable element by Red Flag. He suggests that they release him so he can use his abilities, but Bill doesn’t believe him. Rosen agrees with Bill and leaves Kern where he is.
Cameron tries to search the above-space in the ceiling but his wound starts bleeding.
Rachel wakes up and tries to get free.
Rosen has no choice but to give Bill an adrenaline shot to amp up is system. He tries to lift the blast door but nothing happens. Rosen asks if he wants to use his abilities and points out that Bill’s abilities have always been linked to his emotional state. Bill tries without success until Rosen stops him and says that he has an idea to go on the offensive.
Under Rosen’s direction, the team sprays paint on the walls and sprays creamer and fire extinguishers all around to break up the patterns and make it harder for Griffin to blend in. Gary checks the monitors and spots her going into the MRI room. They go after her but Griffin locks them in while Gary is out of the hallway. They yell at him to get to his office, but he grabs his badge and tells Griffin to come out. She moves in on him, but Rachel arrives just in time to knock her out.
Once they have Griffin tied up, Rosen asks how she gets to them blind spot. She refuses to answer seriously and explains that she’s been following Kern for two weeks. Griffin suggests that they should release her and turn Kern over to them. When Rosen points out that Kern has said the opposite, Griffin asks if they’ve seen cracks in the walls. They realize that there are cracks everywhere and Griffin explains that Kern is using his sonar to crack the walls and break free. Rosen asks who she’s working for and Griffin says that she already has Kern’s research, and she gets a bonus if she brings in Kern himself. She suggests that they let her go and they all come out ahead.
Cameron continues bleeding and Rosen tries to treat him. He realizes that Kern’s vibrations are preventing the wound from closing and caused Nina’s nosebleed earlier. Nina watches and Cameron says that she shouldn’t act like she cares about him. More cracks spread through the building and they go to see Kern. Kern asks what was wrong with trying to bring more Alphas into the world. Rosen gives ether to Bill but the door to the containment chamber is too hot to touch due to reverb. As the building shakes, Kern shatters his handcuffs, goes to the window of his chamber, and shatters it. Rosen and his team are knocked out and Kern walks past them.
Bill recovers consciousness and carries an unconscious Rachel to where Gary is hiding under a desk. Nina is trying to move Cameron, who has lost too much blood, while Bill goes to find Rosen.
Kern approaches Griffin and concentrates on her, demanding to know who hired her. Bill tries to get to them and kern knocks him back. Griffin manages to break free, but Kern knocks her back as well. Meanwhile, Bill loses his temper and his ability kicks in. Kern tells him that it’s too late, but Griffin grabs a piece of broken glass and stabs Kern in the neck. She suggests that Bill go into business as a mercenary but he refuses, and Griffin says that she owes him and gives him a name: Stanton Parish. Before Bill can stop her, she disappears again.
The team cleans up the office the next day and Rosen promises to look into the name. Bill can’t resist teasing Gary, who notes that Bill was a lot nicer when he didn’t have his abilities. Meanwhile, Nina cleans up Cameron’s office and he points out that she cares for him no matter what she claims. When she says she’d have done the same for anyone, Cameron kisses her.
Rosen and Rachel look at what’s left of the containment chamber and they both hope that they won’t be called upon to keep any other prisoners. The doctor points out that Rachel saved all of them, and they figure that Griffin took Kern’s data to her employers. Rachel worries that things won’t get any easier and Rosen doesn’t have an answer for her.