A man driving a farm tractor down a narrow dirt road stops suddenly when he sees a marine helicopter sitting in the middle of a pattern of crop circles in his cornfield.
Kate is appalled to find DiNozzo clipping his fingernails at his desk in the NCIS bullpen. McGee, sitting at his desk nearby, compares getting used to DiNozzo's behavior with the Stockholm Syndrome – the need for a kidnap victim to cooperate with his captor in order to survive. Gibbs enters and orders DiNozzo to get the truck: the team is going to Smokey Corners, West Virginia to investigate the marine helicopter in the crop circle.
When the NCIS team arrives, the marines are already investigating the scene. Marine Lt. Col. Curtis Teague introduces himself to Gibbs and has no apology for contaminating the scene – he has two missing marines to locate. Gibbs informs him NCIS will need to take elimination prints from all of his men, and Teague orders his men to stand down. There is no damage to the aircraft, and it still has 60% of its fuel supply. The helicopter took off at 23:00 for a night proficiency flight, and the flight controller lost the signal 10 minutes out. He was notified of the helicopter's location by the local sheriff just after sunrise. Gibbs orders DiNozzo to sketch and shoot, Kate to bag and tag evidence from the helicopter, and McGee to lay out a search grid of the field. A marine helicopter flies over and Teague tells Gibbs that they've just begun an air search for the missing marines. Teague is ignoring the fact that the helicopter is in the middle of a crop circle, for now, but wants to know Gibbs' thoughts. Gibbs does not believe the marines were abducted by aliens, but he won't ignore anything. Teague gives Gibbs his camera card containing overhead pictures of the site, and tells him that the pilot was Captain Todd Newell, and the co-pilot was Captain Patrick Barnett. The two young pilots share an apartment off-base.
Gibbs hands the photo card to McGee and tells him to send it to Abby. McGee hesitates, as Abby is obsessed with the paranormal - giving her pictures of a crop circle may be distracting. As McGee hurries off to follow orders, Gibbs and Teague agree that they will try to keep this matter from the media.
DiNozzo remarks to Kate that he should have been a pilot as helicopters are "chick magnets." Kate disagrees, telling him that she dreaded traveling on Marine One with the president. DiNozzo nonchalantly scratches his crotch, and Kate scolds him for his "locker room mentality." He is not affected and tells Kate she can scratch anything she wants to in front of him.
Gibbs interviews the farmer, Logan Clay, who tells him that he didn't hear anything strange during the night. The local sheriff, Sheriff Thompson, tells Gibbs that this isn't the first crop circle in the area – a 1994 crop circle was investigated by the Air Force, but they never received any answers. Both men saw bright lights in the sky last night, just like back in 1994. When the sheriff tells Gibbs that he'll ask around about anything strange that may have been seen last night, Gibbs asks him if being sheriff is his full-time job. The sheriff responds that he also runs the local Grain and Feed Store.
Abby is thrilled to receive the pictures of the crop circle, and tells McGee over the phone that it reminds her of Glastonbury in the 1980s. McGee tries to convince Abby that crop circles are hoaxes that he equates with tarot cards and telephone psychics. McGee insists that there is a logical explanation for the crop circles, but Abby tells him that she needs pictures, specimens of the stalks down to the roots, and soil samples. In order to get his cooperation she offers him a look at her new tattoo, and he can't resist.
Gibbs releases the helicopter to the marines, and drives the truck back with McGee and all of his samples, leaving DiNozzo and Kate to check out the pilots' apartment. Gibbs wonders why there haven't been any gawkers to look at the crop circle – this type of incident usually draws a crowd, but the only people there are the farmer and sheriff. As he turns to leave, Teague stops Gibbs to report that his overhead search has found a burnt-out area just north of the crop circle and they go to investigate.
The fire is still smoldering when Gibbs, McGee and Teague arrive at the burned out remains of a small cabin. McGee begins processing.
At the pilots' apartment, DiNozzo and Kate are looking for anything that suggests the two didn't just leave on a routine flight. DiNozzo immediately spots a famous men's magazine, the December 1992 issue featuring Pamela Anderson's debut. Kate leaves him ogling the magazine in the living room and steps into the hallway to see steam coming out through the bathroom door which is slightly ajar. She pulls out her weapon and walks quietly down the hallway. Pushing the door open, she begins to lean into the room when Capt. Barnett grabs her from behind and puts his arm around her neck, demanding to know what she is doing in his apartment. DiNozzo steps into the hallway, his weapon trained on the captain, and commands that he let her go.
Gibbs stalks into the interrogation room and wants to know why Captain Barnett is not cooperating with his team. Barnett curtly tells Gibbs that he was with his girlfriend on Saturday night, had just gotten home to shower and heard someone in his apartment. He denies knowing where Captain Newell is. He says that, if the flight record shows that he and Captain Newell took off last night, that's what they did. Gibbs slams his hand down on the table and advises the captain to give him direct answers. Gibbs leans close to the marine, whispering that their helicopter was found 150 miles away from where it should have been, and that Captain Newell is missing. When Barnett still doesn't respond, Gibbs leans closer and lowers his voice, so that DiNozzo and Kate cannot hear him in the observation room next door. DiNozzo tells Kate that Gibbs is using TBI – truth by intimidation – and begins counting down from 5. When he reaches 1, Captain Barnett starts talking. He says that when the two pilots were leaving for the base, Newell got a call on his cell phone that disturbed him. He said he wasn't feeling well and wanted to call the base to cancel the flight. Barnett tells Gibbs that he doesn't know who the call was from, even though he "rode his ass" to try to find out. Newell just got angry and told Barnett to lay low for the rest of the night, saying that he'd explain when he got back. DiNozzo leaves to pull up Newell's cell phone records.
Abby is excited as she carries a stalk of corn into her lab, and she asks McGee if he felt any sort of energy when he was within the crop circle. Each time McGee tries to get Abby back on task to work on the evidence of the fire she returns to the subject of crop circles, and tells him she is running analyses of the plants within and outside the circles. McGee warns her one more time before leaving her to her obsession.
According to the records at New River, Captain Newell signed the log for the aircraft, but no one remembered seeing Captain Barnett. Newell is an only child and grew up outside Orlando, Florida and there doesn't seem to be anything linking him to West Virginia. His parents died two years ago. Newell does have a record of impulsiveness and fighting. DiNozzo tells Gibbs that the last phone call that came into Newell's cell phone was last night at 21:30, he didn't make or receive any calls after that, and his cell phone is currently off. The call came from a pay phone in Smokey Corners, West Virginia.
Back in Smokey Corners, Gibbs and Kate check out the phone booth attached to a service station and notice a young woman peeking out the window, watching their every move. Inside the store, Ritt Everett, Daphne's father, makes a call, advising someone to get there as soon as possible. Kate dusts the pay phone for prints, but it has been cleaned. Gibbs uses his pocketknife to open the coin container and tells Kate to get the coins to Abby for prints. Everett comes outside to see what the two agents are doing, and tells Gibbs that he didn't see anyone using the phone Tuesday night. Sheriff Thompson drives up and asks Gibbs if he's having any luck with the case. He tells Gibbs that, after asking around he's found that many farmers in the area are complaining that their animals are acting up. Gibbs shows the two Captain Newell's picture, but they don't recognize him, and there aren't any families named Newell in town.
Gibbs gets a call from Abby who is angry because the Air Force won't give her their files on the 1994 crop circles in Smokey Corners. When Gibbs tells her he'll make a call, she insists that it is a conspiracy as big as Area 51. She has found that the cabin fire was arson – the arsonist used gasoline as an accelerant, but she is still working on the debris. Kate catches Daphne Everett as she leaves the store and shows her the picture of Captain Newell.
Watching from inside the store, Ritt Everett and Sheriff Thompson are concerned about Daphne, but, Everett insists, "Long as both sides stick to the story, we'll get through this."
Daphne nervously tells Kate that she can't talk about it with her daddy there, but he will be leaving for the VFW at noon and Kate should come back then.
Logan Cole is watching the make-shift marine field office near his field as the search dogs are being loaded into a truck. Lt. Col Teague reports to McGee and DiNozzo that the search dogs are being called off as something has screwed them up - they began acting up as soon as they entered the woods. McGee suggests that they don't tell Abby about this development, and DiNozzo recounts the plot of "Invaders from Mars," a 1950s sci-fi movie about aliens landing in a field who took over the locals' minds. He calls it the scariest movie that he ever saw. When Gibbs arrives they tell him that all of the locals have the same story about BOLs – "Balls of Light" – that they saw in the night sky. Abby claims that they are created by manipulating the atomic particles in the atmosphere.
Back at the lab, Ducky asks Abby to run a tox screen on a tissue sample from a body exhumed in Arlington. Looking down at the dozens of evidence containers on her lab table containing corn stalks, soil samples and burned debris he sees that she is overwhelmed. He tells her that, since his body has been dead for 36 years, a few days of delay won't matter. She asks him for a second opinion about something she has found on the inside door handle from the burned cabin. Checking the microscope, Ducky believes the slide shows mammalian cells, probably from a human. There was someone trapped in the cabin fire, possibly the marine aviator, but no remains were found.
DiNozzo and Gibbs walk the cabin debris site again, wondering why they didn't find human remains within the structure. Gibbs tells him to get the cadaver dogs up to the site to begin searching for a body. When Logan Clay arrives, he informs Gibbs that the cabin wasn't on his land; the land has belonged to the county since the last owner, Monroe, died. He died in a hunting accident and the track has been abandoned ever since. Kids did use the cabin to mess around. Gibbs only stares at the man, clearly unconvinced.
When Kate arrives back at the service station to speak with Daphne, she doesn't find her. Ritt Everett is waiting for her in the nearby barn, but Kate tells him she only came in for gas. Everett leans close through her car window trying to intimidate her before Kate drives off.
Gibbs goes to the West Virginia State Police to get any information he can about Smokey Corners. Captain Grant tells Gibbs that he doesn't get to Smokey Corners much – they never call in the State Police. He tells Gibbs that there is a feud going on up there, and it has been going on for decades with the east side of the valley fighting with the west side. He was told by his predecessor to stay clear: they take care of their own problems. He doesn't know of any murders that ever occurred there.
McGee is scanning the cornfield with a magnetometer per Abby's request. Kate and Tony laugh about the fact that Abby's new tattoo that she promised to show McGee is actually on her ankle. McGee excitedly kneels down to examine something that has registered on the instrument, and brushes away the corn stalks to find a rubber alien mask with a small magnet buried beneath it. He turns to DiNozzo who makes the Vulcan hand sign at him. Gibbs arrives to speak with Abby over the computer link. She tells him that she found two partial prints on the coins from the phone booth. She identifies one local man named Greg Sikes, and DiNozzo immediately begins a background check on him. Teague arrives with the news that the cadaver dogs have found something. The dogs have led the marines to a shallow grave containing a burned body.
DiNozzo and McGee arrive at Greg Sikes' trailer and, while McGee is knocking at one door, DiNozzo enters through another. The two search the trailer, and DiNozzo finds a half-eaten sandwich. McGee comes up with two strips of photos showing Greg Sikes and Daphne Everett. Back at the lab, Ducky is examining the burned body, and has determined that it is the body of a man somewhere in his mid-twenties to thirties. He also has a bullet wound in his chest. Abby reports that the DNA she found on the door knob of the burned cabin was not Captain Newell's but belonged to Newell's male sibling. The dead man was Captain Newell's brother.
Since the Captain's service record showed that he was an only child, he must have lied about having a brother for some reason. In the lab, Abby is still obsessing over the corn stalks, and is trying to prove that the corn stalks within the crop circle have been changed in some super-human way. McGee tries to convince her that she is looking for something that isn't there. He shows her the overhead pictures of the circles again, showing her that in most of the circles the stalks of corn were bent down in a circular pattern going clockwise, but, in the circle with the helicopter, those stalks were bent down going outward from the center by the downdraft of the helicopter. The corn stalks were still standing when the helicopter began to land.
Kate and DiNozzo find that Todd Newell's mother remarried when he was nine years old, and he was adopted by his step-father. Newell's mother's first husband was named Sikes, and the couple had two boys, Greg and Todd. Todd Newell was born in Smokey Corners, yet never mentioned anything about his childhood to his co-pilot, Captain Barnett. Todd and Greg's father died several years ago in another "hunting accident." Kate and DiNozzo gather their gear to head off to Smokey Corners to try to find Daphne Everett. Before they can leave, McGee brings Abby to Gibbs' desk to admit that the crop circles were bogus. Abby is still not convinced. She wants to know what made the dogs unable to follow the scent trail the first day they searched for the missing marine. Gibbs begins to tell her that the cadaver dogs didn't have any trouble the next day, and then stops. He realizes why they haven't been able to find Captain Newell. He hurries up the stairs to MTAC and explains that only another marine could figure it out.
Gibbs connects to Lt. Col. Teague in MTAC and tells him that Captain Newell is still alive and evading their search. In his SERE training, Captain Newell was taught a technique to evade enemy dogs using GS powder, the irritant used in gas mask simulations. Lt. Col. Teague knows it well; he even keeps a few canisters of it in his vest. When Newell used it on the dogs, it made them useless. The captain would also have pilot night-vision goggles and a survival radio to monitor their searches.
In the car on the way back to Smokey Corners, DiNozzo is driving Kate crazy. He accuses her of having PMS, and then notes that he thought that wasn't until next week. They approach Sikes' trailer hoping to find Daphne there when they see her running out of the trailer and getting into her truck. Kate pulls the car in front of the truck and Daphne tries to run for it. Kate and DiNozzo catch her, and Kate notices that Daphne's face is bruised. They tell her that they know Greg Sikes was her boyfriend, and she admits that she is pregnant. She believes that Greg is hiding from father. They tell her that Greg is dead.
That night, McGee is sitting nervously in the passenger seat while Gibbs drives erratically towards Smokey Corners. Gibbs knows that whatever Greg Sikes said to his brother made Captain Newell break regulations and take a marine helicopter to West Virginia. He landed in the farmer's field because it was the closest open ground to the cabin where his brother was hiding. He arrived too late to save his brother. McGee believes that whoever killed Sikes knew they couldn't cover up a marine helicopter with another "hunting accident" story, so they made the crop circle hoping the military investigation would back off and do the same kind of cover-up the Air Force did in 1994.
Daphne tells Gibbs and Kate that she and Greg were from different corners of the valley, so they tried to hide their relationship from everyone in the area. The last time she saw Greg was at the pay phone at the service station – he was calling his brother for help. The two brothers were reunited when their mother died two years ago - they were the only family each had left. Daphne believes that Captain Newell has been drawn back into the feud, and is going after Daphne's father for revenge. Gibbs orders McGee and Kate to take Daphne out of the area. He calls Lt. Col Teague and tells him to withdraw his men from the area to make Newell believe that the marines have gone. Gibbs is hoping to draw Newell into making a move on Ritt Everett.
Sheriff Thompson and Ritt Everett stand outside the service station and watch the marine trucks leave town the next morning. Ritt immediately goes inside his store and begins loading his rifle. The sheriff tries to tell him that "they pulled it off" and "this thing is going away," but Ritt won't be placated. Everett believes that he has to get Greg Sikes' brother before he gets him.
Out in the woods, Captain Newell watches the marine helicopters fly off and comes out of hiding.
DiNozzo and Gibbs enter the store and confront Sheriff Thompson and Everett, DiNozzo holding his weapon on the armed man. Gibbs tells DiNozzo to read Everett his rights for the murder of Greg Sikes. Everett responds, "Greg Sikes is dead? I thought he went hunting." Gibbs tells the two that the West Virginia State Police are on their way, but he will detain both of them until they arrive.
After nightfall, Captain Newell makes his way towards the small store adjoining the service station using night-vision goggles. The NCIS team is posted around the area, waiting for him to make his move. Newell moves cautiously behind some old cars parked behind the station. Trying to get a better angle, DiNozzo moves slightly in the barn next to the station, and makes a noise. Knowing that Newell made DiNozzo's position, Gibbs calls for the lights, and all of the outdoor lights come on all over the yard, blazing in Newell's night-vision goggles. The team surrounds Newell, demanding that he lower his weapon. Newell holds his gun on Gibbs and tells him that it has always been an eye-for-an-eye in the valley, and this won't end until Ritt Everett is dead. Newell knows he'll never fly again, so he doesn't see a reason to surrender. Gibbs assures him that, since Newell hasn't hurt anyone, yet, he'll do everything he can to help him. Gibbs also tells him about Daphne and his brother's baby. Newell lowers his weapon.
In the NCIS interrogation room, a clean and uniformed Newell explains his family history to Gibbs. He tells him that their mother was always ashamed that she left Greg behind when she moved away from Smokey Corners, but that their father wouldn't let her have both of them. He took the marine helicopter because it is intimidating and he thought it would scare the locals. He arrived too late and the cabin was in flames with Greg trapped inside. Everett and others began shooting at him, and he was hit in the leg. He couldn't get back to the base, and thought that all that was left was revenge.
In the NCIS bullpen, McGee asks Kate who sent her the beautiful bouquet of flowers she is arranging on her desk. She smiles and tells him they are from DiNozzo. He realized that he has been pushing her lately, and sent her the flowers as an apology. Kate is very impressed because they are from her favorite florist. "How did you know?" she asks. "He went through your purse and got the phone number off your PDA," says Gibbs as he walks past.