A typical Saturday morning in the Shannon home. Elisabeth and Josh are headed to work, and Jim is taking Zoe somewhere very special. Maddy claims to have homework to catch up on, but when the rest of her family is gone, she hurries off to meet with her soldier boyfriend, Reynolds. Malcolm discovers that the mysterious container is impossible to open because it is covered in sensors which only react to a single person's DNA. Taylor assumes that the person is Mira, and tells Malcolm to keep the box safe.
Hunter has been feeling kind of off for the past week so Skye takes him to the clinic where Elisabeth does an exam. She finds out that a parasite is living in Hunter's intestine, but it shouldn't be too difficult to get it out. Meanwhile, Jim has taken Zoe to a place known as The Eye, a repository of all knowledge and human history. Zoe wants to see the place where she was born, and Jim shows her an old farmhouse, where Elisabeth gave birth to Zoe in secret.
Maddy and Reynolds are out in a field of wildflowers and they begin to kiss, but their romance is cut short by the appearance of something in the sky. Meteors ram into the atmosphere above Terra Nova and emit an electromagnetic pulse which takes out all of the colony's technology and electronics. The accompanying sonic wave speeds through Terra Nova and causes injuries and lots of structural damage. Maddy and Reynolds are outside the perimeter without a way to get back or call for help, Jim and Zoe are trapped in the Eye chamber, and Elisabeth will have to remove Hunter's parasite the old-fashioned, surgical way. Meanwhile, Terra Nova itself is defenseless against dinosaurs and Sixers.
Malcolm tells Taylor that they do have a chip fabricator which can produce new chips for all the electronics, but the chip fabricator's also damaged from the EMP. Boylan, however, will be able to fix it. Taylor convinces Boylan to help out through physical force. Boylan agrees to fix the fabricator chip, but it will take some time.
Elisabeth begins the surgery to extract the parasite. She cuts Hunter open and fishes out one end of the worm and begins to wind it carefully around a rod. Jim finds out that there's an access panel to the Eye which leads back to the corridor. The Sixers begin to plan their attack while Terra Nova is defenseless. Maddy and Reynolds start their long walk back to the colony, but they won't make it back before it gets dark. Reynolds coats Maddy in some rank-smelling mud which will help mask their smell and keep the predator dinosaurs away. After being stalked by nykoraptors, they climb up a tree, intending to wait there until morning.
Back at the clinic, Elisabeth needs to tend to more critical injuries so she instructs Skye to take over removal of the parasite. She does so, worrying about Hunter's safety because he's the closest thing she has to a real family. Hunter then confesses that he doesn't want to just be thought of as a brother. Skye is surprised by the news and loses her concentration, which causes her to tug too hard and rip the worm in half. The rest of the animal slips back into Hunter's abdomen.
Jim encourages Zoe to go through the access tunnel, but Zoe is afraid of the spiders that might be there. Jim promises that he'll sing the "go away spider" song to chase them off. Zoe is scared but she agrees to go into the access tunnel and unlocks the door, freeing her father. Meanwhile, the Sixers begin to herd a huge dinosaur towards the colony.
Jim meets up with Taylor and they fire flame-tipped arrows outside the gates, creating a wall of fire to chase off the dinosaur. Taylor spots a spear in the dino's back and realizes that the Sixers have brought the dino to the colony as a diversion. Sixers have snuck into Malcolm's lab in search of the container. Jim and Taylor try to fight them off, but one of them escapes with the box.
Boylan has repaired the chip replicator and one of the first chips he manufactures is for the clinic. Skye rushes to deliver the chip back to Elisabeth. She's now able to complete the parasite extraction and save Hunter's life. The next morning Maddy and Reynolds wake up in each other's arms after a fitful night's rest. They hurry to get back to the colony before anyone discovers they're gone.The Shannons all arrive back at home, with Maddy pretending to have been there all night.
Taylor still believes that the Sixers have a spy in Terra Nova and orders Jim to find out who it is. Mira takes the box to another man named Lucas, who claims to have been outside in the jungle for too long. Mira warns Lucas about Taylor, saying that he knows Lucas is getting close to an answer. The box appears to contain research data of some kind. Lucas says that Taylor will have to kill him to stop him uncovering everything, and Taylor still wouldn't do that to his own son. He'll have to make a choice between family and Terra Nova.