The episode begins with Jack receiving complaints from one neighbor about the other hiding something. Jack tells Allison it has been like this for weeks, ever since the news about a spy has spread through Eureka. Doug meanwhile is busy instructing Holly to fill up all the paperwork that is required to be completed, now that she has been brought back to life. Doug tells Zane that the paperwork needs to be done in order to inform all government agencies that, Holly’s death certificate was filed erroneously. Holly then wonders how she should spend her new life. Meanwhile on Jo’s information officials from DOD have arrived to take Grace into custody.
Jo and Jack are informed that the case shall be handled by the justice department and all evidence shall be placed in its custody. They are also informed by the Major that, if there is anyone else involved in the espionage they too will be found. Henry sitting all alone in his garage, meanwhile plays the disk and sees himself talking on the ensuing video. Allison meanwhile shows Jo and Jack the experiment that is being conducted, involving something called ‘smart dust’ which can be used to control temperature and thus global warming. The dust is made visible to Jack and Jo, and they are informed by Allison that the dust is being controlled by a cooled plasma field. The controlled dust looks like a large mirror, and when touched causes ripples on the surface like water.
Allison then informs them that Doug has taken it upon himself to spread the dust over a 200 meter area. They then see Doug flying over their heads in a biplane. Zane meanwhile shows Holly around his lab, so she can do her research on anything that she likes. Zane then leaves for a bit, and the computer in his lab speaks to Holly, informing her that she has one message in her inbox. She asks the computer to play it, and when played, it turns out to be patterns and pixels, which have some kind of a hypnotic effect on Holly, leaving her dazed. The message turns off before Zane once again comes in. She then looks oddly at Zane, but assures him everything is fine. Doug meanwhile spreads the dust over the designated area, and much to Jack’s surprise nothing goes wrong while Doug is doing so.
Holly meanwhile plays back the hypnotic images in the lab, with a trusting Andy as her test subject. Henry meanwhile tells Jack and Jo that he wants to surrender himself, as he is the second spy. He tells them everything that had happened was his fault. They are shocked and ask him why, he in turn tells them that they will have to ask that to the other Henry from the other timeline this question. He also tells them that all of this happened during the trip to 1947. Henry tells them that Grace is sitting in jail because he showed her the way, so if she is being punished so should he. Henry then proceeds to surrender himself to Major Shaw, but Jack suggests that Henry delay his decision till after he has spoken to Grace. Jo offers to arrange a meeting between Henry and Grace.
Holly meanwhile gets Doug to sign a form allowing her to work in the bio-printing lab, although her specialty is astrophysics. Later while driving down a road, Jack and Jo see a car approaching them head on, the two vehicles then stop nose to nose, and out steps Jack and Jo from the other vehicle. Jack and Jo are basically seeing their own reflection, and conclude that it’s all thanks to the ‘smart dust’. Doug later tells Jack that he is mistaken, as the smart dust is only confined to the test area. Doug then finds out that the device controlling the dust has been tampered with. He then tells Jack that the smart dust could affect everything from electromagnetic waves to neural functions. Grace meanwhile convinces Henry not to surrender, and tells Jo to take care of Henry and see to it that Shaw doesn’t find anything incriminating against him.
Andy meanwhile tells Jack that the dust controlling device could have been sabotaged by someone within GD, and hence they proceed to make their inquiries. Doug meanwhile asks Allison to talk to Holly, and see if she is fine, as he is baffled by her choice to work with the bio-printer. Allison later enters the bio-printing lab and sees a body being bio-printed, just like Holly’s was. Holly then comes in and shuts down the printing, and explains to Allison that she is just running some tests. She then politely tells Allison to mind her own business and leave, much to Allison’s surprise. Allison later tells Henry about the work Holly is doing in the lab, Henry too finds the whole thing odd and decides to check it out for himself.
Zane meanwhile shows Allison the message that was addressed to Holly, in which is seen the digital form of a human hand, and also other digital patterns. Zane tells Allison that Holly must have surely seen the video, although she lied to him that she saw nothing. Zane then tells Allison that the patterns in the video could cause epileptic seizures and affect the brain. Allison assumes that the whole thing isn’t an accident. Zane decides to keep digging in order to find a source code to. Jack meanwhile gives Doug an idea that he gave Andy earlier, which could help control the smart dust. Much to Jack’s surprise Doug like the idea, although Andy had dismissed it. Allison meanwhile runs into Henry while he is coming out of Holly’s lab. He looks a bit dazed, but tells Allison that everything is fine with Holly.
He then tells Allison that he had the bio-printer removed offsite for maintenance; hence there is nothing to worry about. Jack meanwhile comes in and tells Allison that Andy is behaving oddly, and asks her if the smart dust could have affected him. Allison tells him that it could have but that doesn’t explain why Holly and Henry are behaving oddly. Jack decides to get on it as soon as he has finished helping Doug get the control unit back up. Jo meanwhile sees the message sent to Holly, and tells Zane that she has seen the video before, when Holly was trapped in the GD computer. Jo meanwhile receives a call from Jack and goes searching for him in the nearby woods. In the woods she hears Jack’s voice but can only see her own reflection thanks to the dust.
Suddenly her reflection begins to punch her, and ultimately begins choking her, much to her shock and horror. Just then Andy comes by and talks to Jo in Jack’s voice, telling her that he can’t help her right now. Later Jo is shown sitting in Doug’s office, with Dough being questioned by Shaw about many of the files that were taken as evidence turning out to be corrupted. Shaw tells Doug that he shall get to the bottom of this. Zane and Allison meanwhile conclude that something else is trying to get out from the matrix. Allison then concludes that the smart dust is being used by someone else to knock out communications, so that they can’t talk to each other or put the pieces together.
Jo and Shaw meanwhile come in and arrest Zane for tampering with the evidence files. Jack meanwhile finds out the place from where the dust is being controlled, with the help of a device given to him by Doug. He then sees the bio-printer nearby printing a body. He is then shocked to see Jo and Henry lying unconscious nearby. Then suddenly, he turns around and is shocked to see Holly standing with a clone of Henry and Jo, along with a smiling Andy by her side. Holly then walks up to Jack and tazes him, rendering him unconscious. The episode ends at this point.