The episode opens with a pan from outer space into a seemingly harmless house. A woman is lying in bed, talking to her husband Walter on an intercom system. The panning then continues on to the basement where Walter is soldering a control panel. He then adds it to a computerized device and turns the device on. He rejoices in the success of the project but his rejoicing soon turns to fear when something goes wrong.
We pan out of the city and end up on a rainy deserted road. The man driving is clearly agitated with the fact that he appears to be lost and his female passenger who is sitting behind a mesh police car like barrier isn't helping. When the passenger asks why they just didn't fly the driver refuses to answer. The passenger then reveals that the 'big bad marshal doesn't like to fly'. The marshal then orders the female to be quiet. Her silence doesn't last long. She makes fun of him for following her across three states and finding her in a city of half a million people but then getting them lost on the way back.
Another car appears to pass them and the female passenger in the back notices that the two occupants of the car are herself and her driver. She attempts to explain that to the marshal who takes his eyes off the road and swerves to avoid hitting a dog. They end up off the side of the road and in a ravine. After the passenger complains about the possibility of starving to death the driver passes her some ketchup packets to eat. The marshal then confirms that paybacks are a ... when he opens the door and literally falls out of the car, which is parked in a tree.
We then switch to the two walking into a two, still talking about the encounter. The marshal stops a young man riding a bike and asks for directions. The marshal then heads to the sheriff's office with the female passenger. We pan inside the office where a deputy is reading a magazine. The deputy identifies herself as Deputy Jo Lupo. The marshal then identifies himself as US Marshal Jack Carter. As he's reaching for his ID badge Jo sees his gun and reacts, sending him sprawling to the floor. The female passenger uses the opportunity to escape from Carter. Carter tells Jo where his ID and Jo pulls it out, seeing that he is who he says he is.
Carter immediately notices that the female passenger, whom he identifies as Zoe, is gone. As he's explaining the situation to Jo an older man walks in with Zoe. The man quickly identifies himself as Bill Cobb, county sheriff. Carter then explains about the accident to the sheriff asking her to hold on to Zoe while Carter deals with the car. After putting Zoe in the hold Carter asks about AAA but Cobb tells him the closest thing they have is a guy named Henry. Jo attempts to get a hold of Henry but he's running an experiment so he doesn't hear the phone. After they hear an explosion coming from the direction of Henry's shop Cobb asks Jo to try again. This time Henry answers and agrees to come get Carter.
As Henry's leaving he notices the couple from earlier, the Perkins, pull into his gas station in an RV. As he's talking to the Perkins Henry notices the RV is full of boxes and realizes the Perkins aren't going on vacation they're leaving town. Henry talks to Walter who changes their story to say they're just taking a road trip to spend more time with his family. Henry then gets in his tow truck as the Perkins boy Brian gets back into the RV. As Brian is eating a shop lifted chocolate bar a strange blue field begins emanating from the back of the RV. Brian backs away from it as the RV begins to disintegrate. We then pan to Susan and Walter getting inside the RV and their reactions to realizing what's happened and that their son is missing.
Then we see Henry pulling Carter's car out of the tree. They talk about Carter's job while Henry asses the damage. Carter asks about Henry's job and Henry says he only likes to tow cars in his spare time. He explains that he was a space shuttle engineer back in the day.
We're then back in the lab in the sheriff's station where Jo is cleaning up her guns and ammo. The phone rings as Zoe is trying to talk to Jo. When Jo breaks out the HazMat gear and heavy artillery the sheriff demands to know what's going on. Jo tells him that there's a situation at Henry's station.
It's off to Henry's station then where Henry is just arriving with Carter and his car. After Carter attempts to take over the situation the sheriff tries his best to keep Carter out of the way. Carter sneaks onto the crime scene any way, where he first runs into Alison Blake. Blake and Carter then struggle assert dominance. When Carter finds a hand print on an inner wall in the RV he runs a finger through it and then licks it, grossing out Blake. He then confirms to Ally that it was only chocolate. He gives her the exact name of the chocolate bar, a Hersey's Big Block with Almonds bar, stunning her. When she tries to brush of her amazement he picks the wrapper off the ground and shows it to her. He then lifts up a nearby seat cushion showing a hidden compartment underneath where Brian is hiding.
Cobb and Blake then have a private discussion about Carter and Blake wins, taking Carter to a bed and breakfast run by another beloved Eureka citizen, Beverly. As they're on their way there Cobb heads out to respond to a call from another citizen, Taggart who shows the sheriff something he found in the woods. It's the missing chunk of the RV and what remains of the Perkin's dog.
We then pull up front of Beverly Barlow's bed and breakfast. Ally and cater have a nice moment before Carter walks away and into the bed and breakfast. When Beverly shows herself he's stunned that Beverly knows all about him. She offers him a bed to sleep in, giving him linen and things for the bathroom so he can take a shower. Carter has an uncomfortable conversation with Beverly before she leaves him.
We're then back in the forest where Taggart found the remnants of the RV. We're introduced to Douglas Fargo, a seemingly insecure nerd and Mr. King, the apparent leader. Fargo explains that an important chip is missing from what they call Section 5 which causes the other man to worry and wonder how that's possible. They decide to keep the theft a secret from everyone. As they're talking they're interrupted by the sheriff. The sheriff demands to know what they're hiding but only gets a blow off in return.
We're then in Carter's bedroom at the B&B where he wakes up naked and finds out that his clothes are missing. He finds them downstairs, Beverly having pressed and cleaned them. She spies on Carter getting dressed. Since Henry's going to be taking even longer then expected Beverly lends him her car, asking him to make sure to have it back before dark. Carter thinks she's joking until he walks out the door and finds her solar powered IT car.
Carter then takes a drive around the town on his way back to the sheriff's office, taking a good look at all the weird goings on for the first time. We then pan back to the sheriff's office where we see Jo timing herself on putting a gun back together. Zoe seems impressed and the two talk about Jo's past. Jo looks out the window and sees Carter arriving. Carter then runs into an autistic boy and has a short conversation with him. Carter then steps inside the sheriff's office where Zoe immediately jumps down his throat for leaving her locked up all night. Carter asks where Cobb is and Jo jumps down his throat, angry at having to spend the night watching Zoe. When Jo storms out, Zoe and Carter have a conversation where it's revealed that they're father and daughter. After a heated discussion Carter walks out.
As he's driving to Henry's he tries to calm his nerves, almost hitting the same dog again. He takes a look at the cement where the RV was parked until the same dog draws his attention again and he follows the dog into a nearby patch of forest. In the forest he stumbles upon a clearing where it appears that the vegetation and animals have been flash frozen. Before he can make sense of it all, Taggart shoots him in the neck with a tranquilizer dart, knocking him unconscious.
He wakes up in the back of Taggart's car. After having a conversation with Taggart, Taggart slams on the brakes, having spotted Lojack. Lojack turns out to be the dog that almost ran Carter off the road twice and led him into the forest. Taggart attempts to shoot Lojack with the same tranquilizer gun but hits another resident of Eureka instead. When carter reads him the riot act Taggart explains, with great lunacy, that he and Lojack are mortal enemies. Carter then bends the cage on the back of Taggart's truck out of shape so that he can escape.
Back in the sheriff's office Jo and Zoe (who's no longer in the holding cell) are looking through personal ads for Jo. Carter walks in; demanding to speak with the Sheriff, wanting to know what was going on in the town. When Carter threatens to bring in outside help Ally walks in. When Ally tries to stop him she has him tossed in jail with Zoe.
We then head home with the sheriff who looks worn and tired. He sits down in a rocking chair by the door and Lojack makes his way inside. Lojack heads over to the fridge as Cobb picks up the phone. As he's talking to Ally on he phone food starts to disintegrate and so does his house, taking part of his leg before the phenomenon stops. Ally rushes to his house and is shocked to see what's going on.
We're then in the Sheriff's office again where Ally and Jo are discussing Carter's credentials. Both Taggart and Jo don't want to bring Carter in but Ally makes the final call, enlisting Carter's help. Ally and Carter go for a drive. Ally presents him with a non disclosure agreement which he signs. They stop at a seemingly broken bridge but when Ally starts the car towards the bridge they drive right over it and continue on to Global Dynamics.
They drive up to the massive complex and Ally gives him a tour. As they're looking around Ally explains that she's the government liaison, in charge of making sure that the work being done at GD is productive. We also get our first look at Section 5 where Ally tells Carter that you need NID clearance to get in there and they mostly do military projects. Ally says she's taking Carter to meet one of their top scientists.
We're then in a forest where four Samurai are doing battle. It's soon revealed that one of the samurai is actually Dr. King and he's working on a project with Fargo. We then see Carter and Ally arriving at an observatory where Carter is introduced to Dr. Warren King. King takes Carter and Ally to where they're storing all the anomalies found related to this case. Carter and King immediately butt heads and it's clear the two men don't like each other.
In the car ride back Carter steps over the line with a personal comment and Ally slams on the breaks smacking Carter's head off the dash board. As they're heading back Carter sees Zoe in Cafe Diem so he heads out of Ally's SUV to confront his daughter. We then meet the man Taggart shot earlier who turns out to be Vincent the owner of Cafe Diem. Carter then tells his daughter that they'll be staying in Eureka for a while until the sheriff gets back on his feet. Zoe gives him attitude and storms out.
Vincent tries to make friends with Carter, asking him if he wants to join their pool on where the next occurrence will be. When Carter sees the map he gets an idea. He heads to Ally's house and is surprised when the autistic boy opens the door. When he tells Ally about the conversation Ally gets defensive about her son and his abilities. Carter shows Ally and King the map. After King gives him a hard time Carter tells him that he wants to use King's pattern recognition software to find the point of origin of the anomalies. King takes the plans to GD to get started on it right away.
We're then back at Café Diem where another anomaly hits, and Eureka suffers its first fatality because of the situation. We're then shown a bed where what appears to be a high level military man is awoken and not pleased to hear about a potential catastrophe happening in Eureka.
We then go to Beverly's house where an upset Walter is trying to talk to Beverly about the problem. It's revealed during their conversation that someone is helping Walter, some one he's never met. Beverly seems interested about the situation but can't get any information because Carter walks in. Beverly makes Carter a drink and she starts coming on to him.
It's morning next then and Carter is fast asleep on the chair he was sitting on with Beverly and Ally and Jo are staring at him. He's informed about the fatality and told by Ally that the point of origin is the Perkins house. They arrive to find out that Walter has locked himself in his basement and won't come out. They find that the basement door is sealed with a keypad lock. Jo gets some heavy artillery and breaks it down. Inside is the experiment with Walter trapped inside. When the machine starts to blow they're met on the stairs by heavily armed military personnel.
We're then shown that the basement isn't the only place the military is and that they've actually attempted to take over the whole town. Perkins house is sealed up and the experiment is moved. Jo arrives and talks to the military man we saw in bed a little earlier, Colonel Briggs, joining his team. Briggs heads over to Ally and Carter who find out that Ally is no longer in charge. Briggs is, and he intends to shut Eureka down.
When they arrive with the experiment back at GD, King explains to Briggs what the machine does. When Carter asks how the machine is even possible Henry comes out from under the machine and tells them about the components of the machine, wondering how Walter could have gotten his hands on next generation military hardware. Carter theorizes it came from Section 5 and King plays dumb again.
While the Military rounds people up we're shown that Zoe has made herself right at home in the holding cell and is even taking a bath in the sheriff's office's tub. We then see other citizens being rounded up as well and taken to several bunkers throughout the town. When Carter tries to leave the commando stops him. Henry tries to bring everyone back into focus and they decide that the best thing to do is make a second rift. The only problem is that part of the math problem has been erased. Carter realizes he's seen the equation before and borrows Ally's car keys. He has Jo take down the guard so he can escape the lockdown.
We then see Carter drive to a bunker where it looks like he's there to see Zoe. He does find Zoe but he also finds Ally's son. He brings them both to GD to try and help them solve the problem. Ally is skeptical that her son can help, but to her amazement he solves the problem.
As things outside worsen, the team makes a second anomaly that cancels out both of them, thus saving the day.
It's morning again and Briggs is leaving, warning them that he's watching them. Ally confronts King about the technology, letting him know that she's looking into the situation. King then escorts the experiment to Section 5.
We're then at Henry's Garage where he presents Carter with his repaired car. Carter then drives into town to pick up Zoe and they bump into Cobb. Cobb shows them the leg that Henry has made for him as well. As Zoe and Carter are heading out of town they have a genuine heart to heart.
We then see Beverly and Susan having a conversation in the Perkin's home. Susan is sure that her husband wouldn't have been involved in what he was without some outside assistance. Beverly tries to deflect this, but Susan vows to press forward with telling someone. Susan then has a drink of tea and starts to have trouble breathing. Susan passes out and dies and as Beverly sets it up to look like a suicide she tells the unconscious Susan that "they" had worked too hard to get someone into Section 5 to lose everything now.
We're then in Los Angeles where Carter is at his desk. Two officers from the Department of Defense walk in and tell Carter that Cobb was actually working for them in Army Intelligence. They give him papers indicating that he's been given a raise and promotion. We then pan back to Eureka and the sheriff's office where Lojack steals a sandwich and the new sheriff of Eureka steps out of a steam shower, Sheriff Jack Carter.
As he's psyching himself up you can hear an explosion in the distance followed by a loud crash as something comes crashing through the ceiling. Without missing a beat Carter looks at Jo and has her call Henry.