Hicks and Nina's attempt to question Dr. Kern, a suspected Alpha and Red Flag collaborator, go awry when they subdue him and bring him to the office. Thankfully, the DoD has just installed an industrial grade detention chamber for such occurrences and, even though he's lost his Alpha ability, Bill is happy things are moving in a more military direction.
During an MRI, Dr. Rosen discovers that Dr. Kern has no optic nerve, which seems impossible since Kern definitely seemed to see Nina and Hicks. It appears that Kern has acute sonar abilities but that's not all—he can also create sonic vibrations, which, over time, can destroy walls and buildings. Very bad news. Also, something, or someone, is following the team all around the office.
Since Nina and Hicks took everything they could find from Kern's office, the team starts to analyze the data. Rachel's keen sense of sight allows her to see something sinister: Kern's vitamins for pregnant women are filled with active human DNA. Dr. Rosen asks Kern about it and Kern admits that his vitamins are designed to create new Alphas. The two of them continue to talk and Kern tries to recruit Rosen into Red Flag to create a future where Alphas and the "unenhanced" can work together.
As more and more things go awry within the office, Rachel's senses pick up a new heartbeat. She follows her senses to the elevator, where she is attacked and kidnapped by someone unseen. Panicked, Dr. Rosen confronts Kern, demanded to know what he did with Rachel but Kern is just as surprised as Rosen that there is an extra person in the building. Kern warns Rosen that the invisible person is very dangerous and offers to help, but the team doesn't believe him.
Rosen deduces that the invisible person must have found a way to move about in the team's collective blind spot. By tapping into a surveillance camera across the street, Gary is able to see the perpetrator, but when Hicks gives chase he is cut with a knife. Nina barely has time to bandage Hicks up, when the team hears gunfire. They follow the sound to find bullet marks in the bulletproof glass around Kern's cell. Kern tells them that a woman lurking in the building is an assassin named Griffin and renews his appeal to help but the team passes.
Rosen decides to go on the offensive by injecting Bill with a serum designed to bring back his powers and having the team coat every surface of the office with substances like mustard and baby powder. The next time Griffin moves, they plan to see her. The ploy works when they see Griffin's footprints moving in the powder. They chase her, but Griffin was ready for them and she locks them in their own offices—only Gary is left to defend them.
With time and options running out, Rachel bursts into the room and clobbers Griffin with a laptop. Rachel had been tied up in an air duct but was able to free herself. With Griffin subdued, the team learns that it is Kern, not Griffin, who is causing all the cracks in the building. Kern breaks out of his cell and goes for Griffin who barely manages to kill Kern thanks to a timely distraction by Bill. Before she vanishes, Griffin gives Bill a mysterious name: Stanton Parish.
The team is left to clean up Kern's mess and hope that things get easier. Meanwhile Nina and Hicks are conflicted about whether or not they should pursue a relationship.
Watch a sneak peek of the season finale of Alphas. Aired: 10/22.
An injured and increasingly desperate Doctor Rosen seeks a final confrontation with Stanton Parish. Guest Staring Summer Glau.