Carter accuses Lexi of being irresponsible when she encourages Zoe to skip school and attend a yoga retreat. Zoe, in turn, is miffed that her father is running her life. Carter's annoyance extends to Lexi's friendship with Chuck, Eureka's radical recycling manager, and their "we are saving the world" superiority.
Eva Thorne continues searching for something. She persuades Zane to work on a very old lock. He does and opens a door into the past and its flawed technology. Unbeknownst to them, he also opens a second entrance to an old military installation through a door in the basement of the Tesla School.
Still angry with her father, Zoe insists that she, Lucas, and their friend Pilar should explore the mysterious corridors. They are deep into the complex and hopelessly lost when they encounter Zane, and Lucas makes a mistake that traps them all behind solid steel doors with fresh air.
While Zoe deals with the consequences of her irresponsible behavior, Carter asks Henry to fix his old walkie-talkie. A panic call from Lexi diverts them to a nearby road where her car is caught in a force field controlled by an unidentified man in a superhero costume.
After a near disaster, "Captain Eureka" frees Lexi. He then activates rocket boots and flies away. Lexi is amused by Captain Eureka's gallantry but Carter fears his antics will hurt someone. He sets out to reveal the masked hero. As Captain Eureka ups the ante by walking through a wall, Carter's search leads him through a collection of Eureka's amazing, but discarded experiments.
Finding Captain Eureka trapped within a wall, Carter calls on Henry. The phasing device the man used to walk through solid objects is unstable. Unless Henry can find a permanent cure, the would-be hero will disintegrate. With the mystery solved, Carter and Lexi realize that Zoe is missing. Carter's out-dated walkie tells Henry where she is but the dangerously unstable phasing device offers the only hope of reaching her before she suffocates.
Wormholes start popping up all over, threatening to rip Eureka apart unless Carter can stop them.