The episode begins with Zane and Jo kissing each other. Later Jack and Jo talk about their matrix relationship and how that had affected Allison and Zane. Meanwhile, Douglas tells his team to shut down the Matrix mainframe. Zane tells Douglas that he is the one who restarted the program. Douglas is adamant that Holly is gone and hence he wants the Matrix gone too. Meanwhile, Warren has come in for the evaluations, and meets Jack and Allison. Warren first meets Dr. Fowler who is the Astraes crew’s particle physicist. Dr. Fowler then shows Warren an experiment, which doesn’t turn out to be too successful. Fowler is redacted by Warren, as he feels Fowler is still suffering from trauma of being in the Matrix program.
It is then turn for Douglas’s review. For that, Warren has planned a game of laser tag between him and Douglas. Meanwhile, Jack and Allison are getting cozy in the medical room. Suddenly Douglas locks his target and is about to shoot Warren, and at the same time something in Jack’s brain tells him to do the same and he picks up his gun and fires in front of him, barely missing hitting a scientist. Jack himself and Allison are shocked by what Jack did. Then Jack drops the gun and asks Allison how he came there, and where Warren is. Jack then tells Allison that he is Douglas; he then leaves saying “I need to find me”. Meanwhile, Jack is in Douglas’s body and is wondering what he doing playing laser tag. He then sees his reflection and is shocked to see Douglas staring back at him. Then Jack as Douglas wins the game of laser tag.
Warren then congratulates him and tells him that he has passed the first stage of his review. Meanwhile, Douglas in Jack’s body comes in, and the two comes face to face. They realize that they have swapped bodies. Allison is then told about this neural swap. Jack in Douglas’s body also gives Allison proof to that effect and she is convinced that they aren’t kidding. Meanwhile, Warren Jack who is in Douglas’s body is taken by Warren for the next stage of the evaluation. Later Allison, Henry and Grace brainstorm as to how they should resolve this issue at hand. Meanwhile, Warren is showing Jack in Douglas’s body, images of clouds, which he has to make sense of, and tell Warren what he sees. Warren is surprised to hear his answers, especially owing to the IQ Douglas has.
Meanwhile, Zane comes in and tells Jack in Douglas’s body that he has found something promising in the Matrix project, and hence it wouldn’t be a great idea to shut it down. Jack in Douglas’s body not knowing what to say tells Zane to pursue it and report back to him. Suddenly, while Douglas in Jack’s body is being tested by Grace and Allison, there is a neural spike, and the two people switch back to their own bodies. So now when Douglas is asked by Warren to recognize the various images, he gives intelligent answers. Warren then satisfied with Douglas’s answers clears him for active duty. Later Henry tells the both of them that he would keep looking for why this phenomenon really occurred. Later, just when Jack and Allison are about to get cozy in bed, Jack swaps his body with Zane, who is in the shower. Just then Jo enters the shower and gets cozy.
Zane in the meanwhile is happy to see Allison on top of him and doesn’t tell her what has really happened. Allison then goes to brush her teeth and seductively tells Jack that she will be right back. Meanwhile, Jack in a naked Zane’s body is at his wits end about how he should deal with a naked Jo coming on to him, as much as he is enjoying it. Jack in Zane’s body then somehow manages to take a rain check and leave the bathroom. Jack in Zane’s body then gives Zane in Jack’s body a call. Zane in Jack’s body all this while is still imagining it all to be a dream. Jack in Zane’s body also tells Zane in Jack’s body that if he touches Allison he is a dead man. Zane in Jack’s body warns Jack in Zane’s body of the same, with Jo. Later, when Zane in Jack’s body is out driving Jack’s car, someone cuts him off and Zane realizing he is Jack gives hot pursuit.
Back in Eureka Jack in Zane’s body is called for the review by Warren. Meanwhile, Zane in Jack’s body stops the speeding vehicle, inside is a beautiful girl who apologizes to Sheriff Jack. Zane acts fresh with her and inappropriately flirts with her, as he knows he is in Jack’s body. Just then he receives a call from Henry telling him to immediately come to the lab, so he can run some tests. Meanwhile, Jack in Zane’s body is being put through some rock climbing which the actual Zane loves. Jack in Zane’s body in the meanwhile, is visibly terrified of it. Later Jo is informed by Allison about what Jack has been experiencing, first with Douglas and now with Zane. Meanwhile, Douglas’s flying robot Martha has gone crazy and is chasing Warren and Jack in Zane’s body. Somehow they get rid of it.
The team then decides to find out what went wrong. Later Grace, finds out that, Jack’s brain function is abnormal, which could be giving rise to all the issues. The solution might be to operate on Jacks brain to rectify the issue, and save his life. They later brief Warren about this issue. Warren isn’t too happy to hear it, as he is not too pleased with the truth being hidden from. He tells Grace and Douglas that after the surgery is completed, the whole team would be redacted. Meanwhile, Jo kisses Zane in Jack’s body, just before the operation, and suddenly in the middle of the kiss Jack is back in his real body, and shocked to find himself kissing Jo. Just then Allison comes in, and so does Zane in his actual body, and they see Jo and Jack kissing. Jack shouts “this is not my fault” in frustration.
The operation then begins, and just as Allison manages to reach the part of Jack’s brain that is causing all of this, Grace sees a spike in his brain activity, and Allison’s body is swapped with Jack’s. Allison in Jack’s body then tells Jack in Allison’s body that she would guide him through the process of removing the probe put in Jacks brain by Allison, with Grace’s help; as leaving the probe behind in Jack’s brain would be dangerous. Jack in Allison’s body then manages to remove the probe from the brain in Jack’s body, successfully. Later, Allison in Jack’s body after seeing the readings in Jack’s brain activity concludes that, the spikes in his brain activity could ultimately cause damage to Jack’s central nervous system. Meanwhile, Henry tells them that he has figured out that, the matrix mainframe not being shut down could be the reason for Jack’s neural activity.
Meanwhile, Zane is shown telling Douglas that Holly might still be alive in the program, as he has recently found out from running the program. Just then Henry comes in and tells them that the program has to be shut down, if they are have any hope of saving Jack. Despite the thought of losing Holly, Douglas tells Zane to shut down the program. Just as the program is shut down, Allison is back in her original body, she then runs to see Jack and finds him lying on the ground. Allison and Grace tell Warren that Jack’s brain is corrupted just like a hard disk, and might shut down completely, and they might lose him. Warren suggests that maybe his brain can be rebooted.
Allison and Henry think it can, by giving his brain mild electrical jolts. The jolt works and Jack is back. Later, looking at their teamwork, Warren decides to not redact the team. Grace later tells Henry that she needs some time off, as she is a bit overwhelmed by all that has happened of late. Later Jack tells Allison that, when his brain was dying all he could think of, was her and the kids. Jack then goes down on one knee and proposes Allison for marriage. Allison says yes. The episode ends at this point.