Nina and Cameron go undercover as a couple to capture an obstetrician who is apparently working with Red Flag. Rosen and Bill get word and go to a new containment chamber that they've added capable of suppressing most Alpha abilities. The whole office is also equipped with an automatic lockdown. Rosen is reluctant to have things go beyond his initial vision, but Bill warns him that they're now government assets. Bill admits that he's lost his ability since his run-in with Joshua Englin and he's fine with that, but Rosen warns that it's not him and that the DoD may consider letting him go if he no longer has his Alpha ability. Gary comes in and complains that some of his recommendations, including automated gas turrets, and Bill gently points out that those things don't exist. His co-worker complains that Bill isn't like he was and wonders why he's there if he isn't an Alpha.
Rachel calls in on the elevator and informs the others that Nina and Cameron are bringing in the obstetrician, a bound and gagged Dr. Kern. Nina tells them that Kern was immune to her ability and they take him to the containment chamber... unaware that an unseen force has emerged from the elevator behind them.
As Rosen prepares to place Kern in the MRI scanner, he suggests to Bill that he can come up with a mixture of adrenaline and steroid that will restore his abilities. Bill says that he doesn't need it. Meanwhile, Nina files a report and Cameron brings her coffee. They wonder what tipped Kern off and Cameron figures that Kern could tell they weren't a happy couple. Nina says that it's a bad idea for the two of them to be romantically involved, and Cameron is unhappy that she told Rosen. She finally tells Cameron that Rosen thinks Cameron would be bad for her, and Nina admits that she's screwed up every relationship they've ever had. Bill interrupts to tell them that Rosen has found something and called a meeting. As they leave, the same unseen forces starts typing on Nina's laptop computer.
Rosen tells the team that the MRI revealed that Kern has no optic nerves even though his eyes function normally. Cameron points out that Kern could see perfectly well and tried to avoid him at his office. Gary complains that someone took his phone and Rachel finds it nearby. He complains that someone opened the data files on it. Rosen tells everyone not to touch it and explains that the DoD believes Kern was doing research for Red Flag. Cameron and Nina brought everything from Kern's office back and Rachel and Gary go to work examining it.
Kern wakes up in the containment chamber.
As Rachel examines the urine samples from Kern's office, she thinks she's hears something outside in the office. She goes to investigate but can't find anything despite her enhanced senses. The best she can do is pick up a heartbeat. When Gary comes over, he tells her that she interrupted him and that he's been in his office. As Rachel goes to her office, something scratches the window glass behind her.
Rosen and Bill go to see Kern and ungag him. He demands a lawyer and they tell him that he's being held as a member of a terrorist group. Kern claims to have no idea what Red Flag is. Rosen has Bill stand Kern up facing the opposite wall and then throws a mug at him. Kern flinches and Rosen explains that he has echolocation and uses sonar to "see." They lock him back up and Kern warns them that it won't end well.
Bill goes back to his office and gives Clay a status report. Clay says that he'll be there in two hours. Once Bill hangs up, he thinks he hears something but dismisses it as imagination.
Cameron comes to see Rosen and asks him to give them a little space. The doctor refuses, saying that he has a responsibility as their psychiatrist and employer. Rachel comes in and says that she found pregnancy vitamins and confirmed they contain active human DNA. Rosen explains that they would cause mutations and birth defects. Before he can pursue the matter, Rachel smells blood from the hallway. They go out and develop that Nina is having a nosebleed.
Rosen goes to see Kern, who uses his echolocation to do an ultrasound and spot a mitral valve prolapse. Impressed, Rosen enters the chamber as Kern says that he took an oath to do no harm. Rosen asks about the vitamins and Kern says that he cares about the future. He reminds him of Renestrin, the drug that interferes with the fetal development of Alphas, and explains that his vitamins are a counteragent. Rosen wonders who will be distributing the vitamins and Kern refuses to answer his question. He says that government agents will take him away and that would be a mistake, and that the Red Flag people who tried to assassinate Rosen were a fringe element. Rosen doesn't believe it but Kern says that he believes in a future where humans and Alphas work together. When Rosen notes that he isn't an Alpha, Kern says he sees a time when the unenhanced could join their cause. Kern refuses to cooperate and says that he won't be going to Binghamton.
Rachel hears someone outside her office and goes to investigate. She hears the same heartbeat from earlier and sees faint footprints in the carpet. Following the trail to the elevator, Rachel goes inside, discovers that the camera lens has been cracked, and someone grabs her.
Bill and Cameron contemplate Kern and try to figure out how to break him. They realize that someone has tapped into the computers and locked them out. Nina asks if they've seen Rachel and reports that she's disappeared. As they call out for her, Gary complains that something has glitched the monitors. They bring up the security footage and track Rachel to the elevator where she disappears off the cameras. They find blood and drag marks, and Cameron notices a crack in a ceiling supports.
Rosen goes to Kern and demands answers. Kern has no idea what he's talking about and tells Rosen that there are eight heartbeats in the building, the same that have always been there. Rosen points out that there are only six of them plus Kern, and Kern asks if things have gone missing. He then warns Rosen that they have an unwelcome guest and asks to be released so he can help them. If Rosen ignores him, things will get worse.
Rachel is tied up and gagged and left unconscious in an air vent.
The team gather in the briefing room and watch Kern yell at them to release him. Rosen figures that Kern is telling the truth about an intruder and Bill talks about how he thought he saw someone earlier. The doctor picks up on that and says that they have an unconscious sense of people around them. Rosen demonstrates the concept of the human blind spot and suggests that the intruder has an ability to insert herself into everyone's blind spot simultaneously, effectively becoming invisible. When Nina points out that there are cameras, Gary says that someone has tampered with the cameras. However, he tunes into a camera across the street and shows them the image on the screen. It reveals a woman in the room with them. Cameron tries to hit her without success and runs out into the hallway, and the woman stabs him before fading away again. The alarms go off and the building goes into lockdown, closing the blast door.
Bill confirms that the intruder has locked them out of the system. Gary panics and tries to break the safety-glass windows, and Rosen calms him down. Meanwhile, Nina treats Cameron's wound and insists that she's not good for him, and Cameron says he doesn't care.
Bill discovers that his gun is gone at the same time that Gary realizes the woman took his phone. They hear gunshots and run to the containment chamber. The intruder tried to shoot through the glass without success. Kern says that the intruder tried to kill him, but Rosen and Bill don't believe him. The obstetrician explains that the intruder is named Griffin, and that Red Flag considers her an unsanctioned variable. Griffin is a mercenary and believes in nothing except money. Kern offers to use his ability to find Griffin and Rachel, but Bill refuses to let him loose. Rosen agrees and leaves with Bill.
Gary is unable to override the systems and get the blast door open. Meanwhile, Cameron's wound starts bleeding again.
Rachel wakes up and tries to free herself.
Rosen prepares the steroid/adrenaline shot to give Bill so he can use his enhanced strength to get the blast door open. Once he injects it into Bill, they go to the door but Bill is unable to amp his strength. Rosen wonders if he wants to become angry and Bill clearly isn't. Rosen says that they need to on the offensive and starts spraying condiments on the walls to create abstract patterns and make it harder for Griffin to find the blind spot. He has Cameron shoot a fire extinguisher and Bill spread creamer powder on the floor, while Gary sits in the middle of the room with his computer and ties into the cameras.
They see Griffin run into the MRI room and go after her, but Griffin accesses the computer and locks everyone in except Gary. They yell at Gary to lock himself away, but Gary takes out his badge and demands that Griffin stop hiding. Griffin closes in on him with a knife, but Rachel shows up and clubs the mercenary unconscious with Gary's laptop.
The team tapes Griffin to a chair and demand answers. She suggests that they release her so she can take Kern with her and let them live. When Rosen points out that Kern wants them to release him, Griffin points out the growing number of cracks in the walls and explains that Kern is slowly using his sonic abilities to bring down the building and escape. She refuses to say who she works for and explains that she already has Kern's research. She wants to take Kern out so she can collect her bonus fee and they all win. Cameron's wound bleeds again and they take him to the lab. Rosen realizes that the vibrations are reopening the wound as well as causing Nina's nosebleed earlier. Nina looks concerned and Cameron tells her not to let Rosen know that she cares about him. A new crack spreads across the wall as the vibrations get wrong.
Rosen goes to see Kern, who defends himself and says that he wanted to bring more Alphas into the world. As the vibrations increase, Rosen gives Bill ether to knock Kern unconscious. However, the reverb effect has superheated the chamber door and Bill can't get in. Before they can come up with another option, Kern superheats the links on handcuffs and breaks them, and then shatters the chamber's bulletproof window. Glass and debris fly everywhere, knocking out the team.
Bill wakes up first and gets Rachel to safety with Gary, who is hiding under a desk. He tells Nina to get Cameron to the blast door before he bleeds out, and then goes after Rosen.
Kern is torturing Griffin to get her to reveal who hired her. Bill arrives and Kern blasts him back, and then blasts down Griffin as she rips free of the tape. Bill gets angry enough to amp up his strength and approach Kern, but Griffin grabs a piece of glass and stabs Kern in the neck. She reluctantly thanks Bill for his help and suggest that he go into business for himself. Bill refuses and Griffin repays her debt by telling him a name: Stanton Parish. She then walks away and disappears before Bill can stop her.
The next day, the team cleans up and Bill gives Rosen the name. Bill then teases Gary, who complains that he's annoying now that he's back to being the old Bill. Bill says that he's glad he is.
Cameron goes to see Nina and accuses her of liking him. She insists that she would have been concerned for anyone who was wounded, and Cameron simply kisses her.
Rachel and Rosen considered the contamination chamber and admit that keeping a prisoner in their office was a bad idea. He thanks her for saving all of them, and they figure that Griffin delivered Kern's data to her employers. Rachel figures that things aren't going to get any easier and Rosen just walks away.