Henry is stunned when his unmanned exploration ship opens and someone falls out. It looks like Kim, but she died two years ago. They take her to GD for observation and realize that "Kim" is an organic computer, created by the original computer's self-preservation programming, designed by Kim and Henry. Tess wants to analyze the data the ship has gathered during its 20-year journey, but Zane (Niall Matter) says the on-board computer was fried; nothing is left. The "Kim-puter" tells them that she is what is left, and begins writing astonishing formulas on the walls of her observation room. This new Kim may contain the secrets of the universe.
Carter leaves others to ponder what Kim is and how to deal with her while he and Jo return all of the stolen items from the junk towers. They drop off Dr. Leiber's boost converter only to find the scientist's charred body. Henry confirms electrocution. At first, it seems Fargo may have caused Leiber's death. Then Zane, trying to link his computer to Kim, barely survives a massive jolt of electricity. Logic points to "Kim" as the cause, but when she suggests they terminate her, Carter has doubts. He knows that dealing with Kim/not Kim is hard for Henry but, with Zane - and possibly the whole town - in mortal danger, he persuades Eureka's supreme problem-solver to work with "Kim" to find an answer, while he works through some of his old demons surrounding her death in the process.
Wormholes start popping up all over, threatening to rip Eureka apart unless Carter can stop them.