On the same day that Henry starts his new job at Global Dynamics, Jack's ex-wife Abby prepares to take Zoe home with her to Los Angeles. Zoe is furious that her father won't fight for her to stay. She's so upset that she's using a personal therapy device called an A.T.S. to confront her anger and fears in a virtual-reality version of Eureka.
Jack is far more heartbroken than he can admit. Adding injury to insult, he gets clonked on the head - hard - by a spinning machine as he checks out a noise complaint at a scientist's home laboratory. His head aching, Jack goes home. He tries to talk with his daughter, but she angrily hurls the A.T.S. at him. Frustrated, Jack returns to his office.
Soon after he arrives, Lupo vanishes in a flash of light. Jack seeks help, but no one in town even remembers who Lupo is. Henry, Allison and Stark conclude that their sheriff's head injury must be causing his delusional belief that he has a deputy. Jack doubts that; instead, he suspects that Lupo is a victim of one of Eureka's science projects. Just as Henry concedes that Jack may be correct, Henry vanishes, too. Fargo and others follow. Jack grows increasingly desperate to stop this hemorrhage of townsfolk.
Allison, who can't remember the missing people, believes that Jack is experiencing a mental breakdown. She sedates him and locks him into the jail cell at his office. Just after he wakes, Jack helplessly watches her vanish, too. He then frees himself and races home to his daughter. He and Zoe are now the only two people left in Eureka. Comparing stories, Jack discovers that her memories from before their argument that morning differ from his. Something happened during their fight that changed reality. Thinking hard, Jack realizes that after Zoe threw her A.T.S. at him, he tried it out himself. Now he must be stuck in its virtual world.
He's right. In the real world, Zoe is frantic with worry as her father lies unconscious in a hospital bed. The therapy device has had unexpected ill effects because of the concussion Jack suffered earlier. Allison, Stark and Henry can't disconnect Jack without risking his death, but as long as the device remains on, Jack will be trapped in its world, forced to play by its rules. To escape, he must thus confront his worst fear - losing his daughter.
Wormholes start popping up all over, threatening to rip Eureka apart unless Carter can stop them.