Zane and Allison are still edgy around Carter and Jo, respectively, because of their matrix relationship. Zane is so driven that he reboots the matrix program that had them all trapped in order to find out why it placed those two in a romantic relationship.
Meanwhile, Warren Hughes, the relationship auditor, is in town to test all of the crew members' fitness to return to their jobs. Fargo's up first, but midway through his assessment, he loses his mind – literally! Fargo's consciousness switches into Carter's body, and vice versa. Carter barely makes it through Warren's questioning, when suddenly, their consciousnesses switch back to their rightful places. No one knows what caused the switch, but they're relieved things are back to normal. Allison is grateful she gets to go to bed with the man she loves, but she's not lucky enough to wake up with him, too. This time, Carter's mind jumps into Zane's body, just as the latter is taking a shower with Jo!
When Zane figures out what happened, he's furious, and Carter tries to explain the situation, but there's no mollifying a jealous man after you've seen his girlfriend naked. And when Martha, the flying security robot, goes nuts and attacks Warren, they realize that there might be multiple factors at work. After Carter has another neural analysis, they discover that he has a cluster of axons that may be acting as an antenna for other peoples' consciousnesses. Allison preps for surgery but just as she's in the midst of it, her mind switches with Jack's. She manages to guide him out of his own brain, and they continue to search for solutions.
Jo, unaware of the latest switch, tries to clear the air with Carter, but inadvertently tells Allison that she has, from time to time, entertained the thought of being with Carter. Allison, posing as Carter, states that the sentiment is one-sided.
Henry comes to check in on Carter, and tells him that there may be a link between Martha and all the body switching – if there's some energetic frequency affecting the robot, the same frequency could be affecting anyone involved in the matrix program. Carter realizes that it could be the matrix program, itself, that's emitting the frequency. He runs to the matrix lab where Zane is just then telling Fargo that the consciousness of Dr. Holly Marten is still active in the program. Fargo is faced with a horrible decision: shut down the program and lose Holly forever, or keep it running and lose Carter, and possibly others?
Ultimately, he orders the program to be stopped, and though it breaks his heart, he knows he has to let go. Everything seems to be back to normal, until Carter collapses. The shock of disconnecting the matrix system from his brain is causing his brain to shut down, but Warren comes in with a brilliant idea: they can "reboot" his system with a simple electrical charge. It works, and Warren's observation of how well everyone works under pressure is proof enough for him that they're all ready to return to work.
The pressure of this latest escapade took its toll, however. Grace tells Henry that she needs some time away from their relationship, and Carter, at the opposite end of the spectrum, proposes to Allison, and she accepts.
The cast and creators of "Eureka" help you reacquaint yourself with your favorite characters.