Dale "Barbie" Barbara buries a man's body in the woods of Chester's Mill. As he is leaving the town, an invisible barrier descends on the borders of the township. Local newspaper reporter Julia Shumway, who was investigating mysterious propane deliveries, takes a special interest in Barbie after he saves the life of teenager Joe McAlister, whose parents are trapped out of town. Town councilman James "Big Jim" Rennie makes an emergency radio announcement, while police chief Duke Perkins and his deputy Linda Esquivel try to quell the rise of panic in the town. Big Jim's unstable son Junior kidnaps Angie McAlister when he begins to suspect she had an affair with Barbie. Carolyn Hill and her partner Alice Calvert are passing through Chester's Mill with their daughter Norrie when the barrier appears and Norrie has what they think is an epileptic seizure. Julia takes Barbie into her home, where he realizes the man he buried was her husband. Duke suggests to Linda that the entire town is being punished and is about to reveal a dark secret about the town when his pacemaker explodes as he approaches the barrier. The U.S. military descends upon Chester's Mill as the world learns of the phenomenon.

When Barbie realizes he left his dog tags at the cabin where he killed Julia's husband, he heads back to retrieve them but is ambushed by Junior, who believes Angie is involved with him. At the radio station, Dodee and Phil pick up a military frequency discussing the dome and Julia commandeers the microphone to broadcast the information. While exploring, Joe and his friend Ben notice that the military is testing to see if water can get through the dome. Meanwhile, Big Jim has Reverend Coggins destroy the propane shipment records at Duke's house, but Coggins accidentally starts a fire while burning the evidence. Linda hears Coggins yell for help and pulls him out of the house, but the fire spreads when a nearby propane tank explodes, forcing the town to form a bucket brigade. Big Jim, who had ignored Coggins' cries for help, uses a tractor to contain the fire. Moments later, a hysterical Deputy Paul Randolph shoots his gun at the dome, but the bullet ricochets off it and kills Deputy Freddy.

Deputy Paul Randolph, locked up after accidentally killing Deputy Freddy, escapes his jail cell and locks Linda inside. Big Jim organizes a search party to find Paul by recruiting other townsmen and Barbie, while Linda resolves to find Paul on her own. In the woods, Paul sneaks up on Barbie and Big Jim to hold them at gunpoint, and Linda shows up and shoots Paul. Big Jim designates Linda as the new Sheriff. Julia tails Junior into the tunnels under the cement plant, where he is looking to find a way out. Junior hits the barrier of the dome. Meanwhile, Joe and Norrie find themselves in the middle of a party as Ben invites everyone in town to charge their electronics using Joe's generator. The party ends when the generator blows. Norrie and Joe touch hands and start having simultaneous seizures, repeating the same cryptic phrase "pink stars are falling."

After Julia learns that Phil and Barbie are connected to her husband Peter, she questions Phil about Peter's whereabouts, but he passes out from an unexpected illness. As other townspeople including Linda begin to display similar symptoms, Alice volunteers her help at the clinic and discerns the town is suffering from meningitis. Junior enforces a quarantine of the clinic and pacifies the panicked patients attempting to break out. With a waning supply of antibiotics, Big Jim and Barbie head to the pharmacy but discover Reverend Coggins had already taken all the medicine, believing it was God's plan for the infected to die. Big Jim retrieves the antibiotics to treat the diseased while Barbie tracks down Julia at the cabin where she had followed leads to uncover documentation of Peter's bankruptcy. Meanwhile, Joe and Norrie experiment with their simultaneous seizures while Big Jim finds Angie in the underground shelter.

Despite finding Angie in the shelter, Jim leaves her locked up, unable to believe his son would do such a thing. Meanwhile, the military has scheduled a visitors' day for the residents of Chester's Mill, where family members of people trapped in the dome can come and visit their loved ones at a designated spot along the barrier. Barbie finds out from a soldier that the military plans to attempt to destroy the dome with a missile, which will likely kill everyone inside. Big Jim orders everyone to take shelter in the tunnels underneath the city. He then releases Angie from her captivity, and Junior sets off after her. As most of the town prepares for the inevitable, Joe and Norrie search for Angie, Junior finds Angie at her house and they spend what they believe will be their last moments together. As the missile approaches, Norrie and Joe share a kiss. The missile impacts the dome, laying waste to everything outside of it but leaving the town unscathed. As Big Jim investigates the edge of the dome, he is approached by Reverend Coggins, who is killed when Jim pushes his head into the dome, causing his hearing aid to explode.

After the town's water tower is inadvertently destroyed and the lake is found to be polluted, Barbie helps Linda stop the looting that breaks out in response to the waning resources. Angie tells Rose about her captivity by Junior and asks for her help, but they are accosted by the Dundee boys who loot the diner, killing Rose and knocking Angie unconscious. Barbie intervenes to rescue Angie and a rainstorm occurs and ends the chaos. Following his trade with Ollie Densmore for the town's use of Ollie's well in exchange for propane, Big Jim gives Angie the offer to protect her and Joe as long as she keeps her imprisonment by Junior a secret. After Julia and Dodee speculate that the source of the radio signal jam could be the answer to the dome's origin, Dodee fashions a radio direction finding device that leads them to Joe and Norrie, who are on a search to find insulin to save Alice. The teenagers shock Julia and Dodee when they show them the video of their seizures and end the signal jam by touching the dome together.

Feeling threatened with his authority, Big Jim takes matters into his own hands. Julia's friend, Harriet, touches the dome and goes into labor so Julia takes her to the hospital. They are gas-jacked by the two Dundee brothers, but Barbie arrives and the two flee. Barbie then takes the woman in labor to Alice to help them. While that's happening, Junior and Big Jim argue about Junior disturbing Angie. Junior goes to the police station and goes with Linda to find the two murderers. Junior realizes that they are at an abandoned house and gets told by Linda that one of them almost raped Angie. Linda kills one of the brothers during a fight. Junior kills the other for the attempted murder when he tries to escape. Big Jim then checks on the city's stockpiled propane; however, he is stopped by an armed thug. Joe and Norrie try to find the center of the dome, finding a second mini-dome that holds a mysterious egg in it. Alice has a heart attack and dies in Norrie's arms. In the mini-dome, the egg's shell begins to light up, with pink-colored lights on the surface of the egg.

At night, Junior comes home but Big Jim points a gun at him and tells him to leave. The next morning, Big Jim confronts Ollie and gets Barbie, Linda, Junior and Carter to take the well from Ollie. As Jim is rounding up volunteers to attack Ollie's farm, Barbie and Linda plan to blow up the well so that the other well's water will return. Jim then realizes that Barbie is going to go ahead with bombing Ollie's well. While everyone realizes that the well has been destroyed, Junior appears and knocks Jim out with his gun. Big Jim is dragged into Ollie's living room and Ollie's men leave saying that they no longer need his water. Ollie then gives permission for Junior to kill Big Jim but instead, Junior asks Jim questions about his mother and upon hearing the truth about his mother's death, Ollie draws his gun to kill Big Jim and Junior shoots and kills Ollie. Big Jim and Junior then reconcile before parting ways. At the police station, Linda is surprised to see Junior back and he tells her what happened. Joe tells Julia about the mini-dome and the egg and both go to see it. It is then hinted that Angie may also be connected to the dome as evidenced by the camera panning across her shoulder blade to show a tattoo of a butterfly.

Julia takes Barbie to see the mini-dome and the egg, but they have both disappeared. Barbie and Linda find a highly strung out drug addict who is undergoing withdrawal symptoms from Rapture, a drug that he had purchased from Reverend Coggins. A thorough search by Linda and Barbie uncovers drug-making equipment in one of Reverend Coggins' coffins. Angie takes over the diner, and tells Big Jim to give her the diner's deed, free and clear. Junior brings Angie back home after a seizure similar to Joe and Norrie's. Norrie notices Angie's butterfly tattoo and wonders if she is the "monarch". Junior takes Angie to his house and shows her a painting his mother made before she died, that was of him as a child with pink stars falling around him. Julia tries to borrow the directional antenna from Dodee but Dodee says that it isn't working anymore. Big Jim receives an unexpected visitor – Maxine, a business partner who created Rapture. She was trapped under the dome because she had decided to pay Big Jim a visit on the day the dome fell over Chester's Mill. Maxine visits Big Jim and Barbie, and before Big Jim can introduce Barbie, Maxine walks up to Barbie and kisses him, revealing that she and Barbie are old acquaintances. Maxine blackmails Barbie into joining her and Big Jim and threatens to tell Julia that Barbie killed her husband. The egg disappears from its location and Joe and Norrie find it in the barn at his house. Angie reveals to them that Joe brought it home at 3 am. Angie kneels down and puts her hand on the mini-dome, and as it lights up blue, Joe and Norrie follow suit and as they're touching three quadrants, a blue handprint illuminates and they realize they need a fourth hand.

Linda takes Julia to help investigate Duke's involvement with previous criminal activity in Chester's Mill. During their investigation, Linda finds a note from Duke saying that after his son died from a drug addiction, he vowed to get drugs out of the town by making a deal with Maxine; he and others bought the propane she needed, and she would keep drugs out of the town. She finds out that Barbie killed her husband, but she interprets it as Peter wanting to die due to his overwhelming debt. Big Jim finds a house on a nearby island that Maxine is supposedly hiding at, and finds the house's caretaker Agatha, revealed to be Maxine's mother, having given birth to her young. Joe, Angie, and Norrie touch the mini-dome in their barn simultaneously. The dome then reveals a fourth handprint. Angie shows Norris and Joe a painting Junior's mother made of a dream she had, depicting Junior and "pink stars falling in lines." The three then take Junior to the barn, and as the four of them touch the dome, the egg in the middle releases pink stars all over the barn walls.

Big Jim turns the town against Barbie forms a manhunt after the truth about his past is revealed. Junior decides to leave the three and forget about the mini-dome. As funnel clouds appear and grow, the wind picks up a bench, which almost hits Angie, but is saved by Junior. The clouds then subside. Junior and Angie then realize that the dome wants him to stick with the three. Julia is shot by Maxine, but as the clouds subside, and Julia's heart begins to beat again. Later, Barbie gets Big Jim's help to take down Maxine without any death. The two head to Maxine's underground club and the power then goes out from Barbie's activated alarm. Barbie and Big Jim then steal their guns and lead them outside. Big Jim kills both Maxine and the gunman, and tries to shoot Barbie, but fails. Big Jim accuses Barbie of killing the two to Linda. Norrie, Joe, Angie and Junior touch the bigger dome at the same time, and see a vision of Big Jim bleeding from three stab wounds and a bloody nose. The vision then has the four holding four bloody knives. The other three then consider that in order for the dome to come down, they have to kill Big Jim.

As Barbie hides in the woods, Big Jim gives a speech to the townspeople convincing them to continue the search. During the radio transmissions, Dodee remembers what happened to her when she touched the mini-dome. She takes Big Jim to the radio station and tells him about the egg in the mini-dome. Big Jim hears the people on the transmission discuss past events that occurred in the dome, including Reverend Coggins's murder. Dodee overhears this, and realizes that Big Jim was responsible for his death. To show Jim that she is still trustworthy, she tells him about the egg. Big Jim ends up killing Dodee and burning the station, blaming Barbie for arson. However, the egg is no longer in the barn; Joe's friend Ben has hidden the mini-dome in his house. The mini-dome is forced to be covered in blankets after a piercing noise begins. Ben, Joe, Norrie, and Carolyn take off the blankets to find the dome glowing orange. Julia wakes up with Angie helping her recollect. Big Jim walks Barbie to the front of town hall, where many angry townspeople wait for Barbie's guilty plea. He pleads not guilty.

The monarch hatches, and the butterfly starts flying around inside the mini dome violently and creating expanding black spots where it crashes against the surface. These spots are mirrored in the big dome and begin to expand, casting the town into darkness. Junior, Angie, Joe, and Norrie then touch the dome together, the mini dome shatters releasing both the egg and butterfly, where they discover that the Monarch is Julia. They receive a visit from one of the dome's people. The visitor states that they have taken Alice's form to "bridge the divide", and that the reason for the dome is to protect them. Big Jim puts Barbie in a noose and then Julia has to choose to save the egg and the lives of the town, or save Barbie by giving the egg to Big Jim within one hour. She chooses the egg and protects it by throwing it into the lake. The egg starts to glow, and pink stars rise to the sky, where they remove the dark black "curtain", replacing it with a curtain of piercing bright white light.

Barbie's fate is left in the hands of Big Jim and Junior, after being falsely charged with numerous crimes. However, the dome releases a sound, which causes Linda to halt the execution. The dome has become magnetized, causing observers to pass out. Linda is killed from being crushed against the dome's wall by a vehicle. Meanwhile, Julia meets Sam Verdreaux, while rescuing a mysterious girl from drowning. To save the rest of the townspeople, Barbie meets Rebecca Pine, a high school science teacher who has theories about the dome. Big Jim thinks the dome is telling him to sacrifice himself, and he asks Julia and Barbie for assistance. Julia refuses to follow through, and she prevents Big Jim's death by cutting the rope. The townspeople begin to wake up. Later that night, Angie sees the girl who was rescued and follows her to the school, where she is seen looking into a locker. Angie looks to see what is inside, before she is cut down by an unseen assailant.

Having been spared by the dome, Big Jim starts to have a change of heart, and becomes less selfish and genuinely helpful towards the entire town. Rebecca takes action after a caterpillar infestation begins to take control of all the town's crops, by burning fields, and enlisting Big Jim and Barbie to spray the fields with pesticides. The fuel runs low on the airplane, however, Big Jim helps Barbie by revealing a secret reserve tank. Following Angie's murder, there is a manhunt for the person responsible for the crime. Initially, the girl who was rescued by Julia is the main suspect, as her shoe print was found near the crime scene, however it is soon revealed that it was a man who did the deed. Junior heads to the prison cell to kill the mysterious stranger, before being stopped. Junior then heads to his Uncle Sam's shack to reveal that the previous night, he was drunk, and he believes that he may have been the man who killed Angie.

Rebecca and Big Jim decide to conduct a census on the town to decide how to apportion resources. Chester's Mill is faced with red acid rain and all are forced to stay indoors. At the school, Joe, Norrie and the unknown girl detect a short-lived internet connection. Junior receives a message from his mother telling him that she is alive and to trust only the town's barber, Lyle. Rebecca and Big Jim are going to the school to test a sample of the rain when they are attacked by Lyle. Lyle tortures Rebecca to try to make her agree that they must accept their fate. Barbie, Sam and Julia save Big Jim, and then set out to find Rebecca. Meanwhile Joe, Norrie and the unknown girl open the locker that Angie closed just before dying, they find nothing. They later come across a photo of the unknown girl during the 1980s and find that her name is Melanie. Junior demands answers from Lyle, who tells him that in time he will have all his answers.

With Big Jim on board, Rebecca pushes ahead with the plan to reduce the population. Rebecca discovers a pig that died from the flu and gets blood from the carcass. Liking the idea of using natural selection and letting the virus do the work, Big Jim heads to the diner to contaminate some water. Julia connects the deaths to Rebecca's plans and believes that the diner will be the contamination point. They go there and stop Big Jim but he doesn't have the virus. Rebecca didn't trust him and she takes the virus to the church. Both Big Jim and Rebecca are locked up in jail. Lyle shows Junior postcards he had received from Pauline since helping her fake her death. They go to Sam's cabin looking for Pauline's journal. When Barbie finds Joe, Norrie, and Melanie, they tell him about the internet at the school. They all begin looking through old newspapers and find an article about Melanie Cross' disappearance. In 1988 she, Pauline, Lyle, and Sam found a meteorite with the egg. Melanie was pushed and killed.

As Julia is explaining the trial of Big Jim and Rebecca, one of the men in the crowd pulls out a gun. Phil shoots and kills the man, before heading to the cell block to free Big Jim and Rebecca, but Big Jim tells him that the town would kill him if he were released. Julia organizes a food program, but the storehouse is burned in an explosion. Junior tells Sam about the four hands, and believing that if all four hands are dead the Dome will come down, Sam almost smothers Junior, but stops when Junior wakes and tells him he loves him and that Uncle Sam is the only family he has left. Carolyn, Norrie's mother, finds a back store room where Phil hid the food and he attempts to kill her, but Barbie shoots him in the shoulder. In addition to the hidden storeroom food, Andrea, the widow of a survivalist, shows Julia her massive food supply which should last the town for months. At the diner Julia announces that they must forgive the past and frees Big Jim and Rebecca. Junior, Rebecca, and Sam find a mysterious tunnel leading from Melanie's old school locker.

Barbie and Sam investigate the tunnel behind the school locker, but an explosion causes a cave-in and cuts them off from Junior. Meanwhile, a dust storm brought on by the acidity of the red rain overtakes the town. Julia helps Barbie rather than focusing on the weather crisis, while Big Jim regains the townspeople's support. He eventually convinces the people to build a mist-dispersing windmill, which calms the dust storm. Below ground, Barbie and Sam explore a cave system, eventually reaching a chasm, which they reason must lie outside the dome's boundaries. The two reminisce about the past, and Barbie sees the scratches on Sam's shoulder and realizes Sam murdered Angie. He warns Barbie that the dome will fall when the four hands are dead, and leaps into the chasm. Julia and Rebecca blast through the cave-in, rescuing Barbie. Meanwhile, Joe, Norrie, Melanie and Junior hide from Lyle, and recover the egg from the lake. The stars take on a shape of an obelisk standing in Melanie's hometown, Zenith.

Barbie awakens in Zenith after falling from the cliff edge under the school in an effort to recover Sam's body. He returns to his apartment for some money and is confronted by armed men from his past, who demand that he complete a job he didn't finish. He leads one of them to the target, his father's home, but subdues the man and reunites with Don, his father. Meanwhile, Big Jim decides to hold a memorial service for Barbie at the diner when he learns from Rebecca that he had died and invites the townspeople. Now in Zenith, Sam reunites with Pauline and tells her about his experience in Chester's Mill, and learns her reason for faking her death, and that Lyle is alive, but unresponsive. Julia decides to return to the cliff edge with Joe, Norrie, and Melanie and watches on as Joe flies a drone down the cliff edge. The drone disappears, and they discover an image of a playground and an obelisk on the drone's video, making them believe that Barbie may be alive. Barbie learns about the dome situation, and then convinces his father to help him return to it.

Barbie decides to enlist the help of his father to send a message to Julia, but his father has the message altered. Julia receives the message but believes it may not be from Barbie. After discussing the message with Joe, Norrie and Melanie, she decides to respond in a way that only Barbie understands. In Zenith, Barbie is told that his father had doctored the message to Julia. Believing that his father's computer may have answers, Barbie breaks into it with the help of Hunter, one of his father's employees, and discovers the truth. At his father's company, Aktaion Energy, Barbie sends a cryptic message to Julia telling her that he's alive. He tells her to meet her at the dome edge. With Hunter's help, Barbie assumes a false identity of an Aktaion Energy employee and makes his way through the checkpoints to the dome. Meanwhile, Sam and Pauline talk with Lyle and tells the two men about the red door. That night, Barbie reunites with Julia at the dome wall and gives her a message. She watches as armed men capture him.

Barbie is interrogated by a private company hired by Don Barbara's company Aktaion Energy and is asked about the egg. Don decides to send a message to Julia and threatens Barbie's safety should she not hand the egg over. Barbie is able to escape by knocking out a guard and makes his way to the Hounds of Diana headquarters and reunites with Sam, Lyle, Hunter and Pauline. After Barbie reveals that Sam killed Angie, Sam and Pauline talk, but she blames herself for his actions. Back at Chester's Mill, Big Jim decides to make a deal with a guard at the Dome wall that guarantees safe passage to Zenith for Junior and himself in exchange for the egg. The group decide to return to Barbie's former home and discover the red door that they believe can return them to Chester's Mill. They make their way inside the root cellar and are each enveloped by mist and experience a vision from their past. They awaken in a lake in Chester's Mill, and Pauline decides to return home and meets Big Jim.

Big Jim is still shocked and dumbfounded to find Pauline alive and is angered when she explains that she faked her death. Barbie and Julia prepare the residents for an evacuation and discuss the situation in Zenith. Julia believes she should go first and negotiate for safe passage, but Barbie believes it to be unsafe. They are unaware that Big Jim had met with the men at the dome's edge and has his own deal set up. Barbie discusses his vision while returning to Chester's Mill, that of him as a boy and a red door; he realizes Melanie is his sister. Junior brutally attacks Sam for killing Angie, but is convinced by Angie's apparition to spare Sam's life. Melanie decides to hide the egg in Big Jim's bunker with Junior's help. When the egg emits a high pitched scream, Pauline is faced with crippling headaches. Big Jim locks her inside the house, and when he tells Joe and Norrie of the effect the egg is having on Pauline, he forces them to throw it over the cliff edge. Big Jim returns home and learns Pauline's headaches have stopped, but she is disappointed with what he has done with the egg.

The dome begins to rotate, which shifts colder air down, sending Chester's Mill into a deep freeze. The townspeople take shelter in the school to stay warm, and Rebecca and Sam tend to the ill. Barbie and Julia are in an ambulance on the way to pick up food when the vehicle overturns, resulting in a piece of metal lodging in Julia's leg. After becoming unconscious due to the extreme cold, Barbie carries her back to town and manages to revive her just in time. Big Jim heads down to the dock to look for fuel for the heating generator, when he stumbles upon Lyle in the lake, and rescues him. The dome rotates back by the next morning, and the temperature starts to moderate again. Joe and Norrie grow suspicious of Hunter and follow him to the dome's edge, where they see him communicating via written messages with the head guard. The two teens confront Hunter afterwards, who explains that he was giving the guard false information so that the men will leave Chester's Mill alone. The dome then starts contracting inward.

The dome continues to slowly contract, causing more damage. Junior and Lyle review Pauline's notebook, looking for any clues that might be helpful. Melanie's condition continues to worsen and Rebecca gives her a blood transfusion. Barbie takes Hunter to the edge of the dome and talks to his father, convincing him that Melanie is alive within the dome and the only way to save her is for him to return the egg to Chester's Mill. When Barbie's father tries to take the egg to the red door, the men in black stop him, saying they have orders. Big Jim encourages Pauline to paint, even though her visions have stopped. To save Melanie, all seven hands touch her but nothing happens. Rebecca realizes that Melanie counts as two hands, representing the past and the present. When Sam and Junior hold both of her hands, she recovers, but the ground opens up and Melanie is sucked into a hole. Pauline is distraught but Big Jim tells her she was only trying to help. However, Lyle stabs her in the back, and Big Jim stabs him in a fit of rage.

Barbie and the others wonder how to explore the crater. Joe, Norrie and Hunter go down into the crater and explore the cave, reporting their findings to Barbie, and the townspeople start heading toward the crater. Sam determines that Pauline will die unless she gets surgery. While Pauline is alone with Rebecca, she begs to be given a morphine overdose. Rebecca does so and Pauline dies. Big Jim sees Rebecca with the morphine needle so he kills her. He speaks to the dome, demanding it bring Pauline back to life or he will kill the dome's hands. Julia is called away from the crater, lured by Big Jim who has taken Andrea prisoner. Big Jim kills Andrea and attacks Julia, but she stabs him in the foot and runs, meeting Junior and Sam in the woods. Junior confronts Big Jim and shoots him in the shoulder. He runs to the crater, leaving his father in Chester's Mill. Barbie crosses a crevice in the cave, but Julia is unable to follow when the crevice widens. Barbie goes ahead and catches up to the townspeople, and they end up at a wall. Barbie touches the rock and it crumbles, revealing Melanie.

Taking up where the previous season left off, inside the tunnel Barbie and the surviving townspeople follow Melanie into the white light. Then they magically appear not only outside the tunnel, but outside the dome which quickly shatters. Barbie runs back for Julia and finds Big Jim, Junior, and Julia dead. One year later Barbie is working in the Middle East as a mercenary with Hunter as his surveillance specialist. Barbie has a new girlfriend, Eva Sinclair. Norrie is in college and is pledging at a sorority. Her mother Carolyn is happy for her. Sam is in prison and going to AA meetings. Joe is living with his parents and having trouble adjusting. FEMA sent a therapist, Christine Price, to Chester's Mill to help the townspeople recover from the event and "move on" with their lives. Meanwhile back inside the dome, Big Jim, Junior, and Julia are squabbling as usual.

Julia and Junior determine that they need to cross the crevice in the tunnel and see what is on the other side. After doing so, Junior crosses into the light and becomes part of the alternate world, and sees what his life is like without his father. Barbie gradually becomes aware that they are in an alternate reality. Barbie's father convinces his superiors that he should take the egg back to Chester's Mill. After he does so, he is met and strangled by Melanie, who then takes the egg to the tunnel. Julia sees that all of the townspeople are really within pods that are connected together. Melanie attaches the egg to the main central pod, which is somewhat larger than the others, and it begins to emit a pulse of pink energy, flowing towards the other interconnected pods. Big Jim arrives on the scene and destroys the pulsating egg. The townspeople emerge from their respective pods, and Eva Sinclair and Christine Price are among them.

The townspeople return to the surface and resume their lives, still under the dome. Junior is particularly upset by returning to life under the dome, and decides to stand up to Big Jim by setting fire to their family home. Julia presses Barbie for details about his relationship with Eva while in the pod. Barbie is initially reluctant to discuss it but eventually opens up because the whole thing was imaginary. People begin to notice that they have changed somewhat after emerging from the pods. Christine and Eva begin to discuss their mission, and how the Egg was preparing the townspeople before the process was interrupted. Eva also wonders whether she is pregnant by Barbie. Melanie's usefulness is done and she is killed by Christine. Frustrated, Big Jim decides to leave to the island on the rowboat. Julia and Barbie spot Eva, who is real after all. Christine starts a counseling practice and recruits Sam to assist.

Big Jim is captured and questioned by Aktaion agents. Food becomes an issue in Chester's Mill, and Barbie and Eva go out and locate three silos full of cattle feed, which can be turned into something edible. Julia becomes suspicious of Christine when she lies about her badge, which came from Aktaion. The townspeople start to revert to their original selves, and Christine tells Joe about the importance of keeping the "kinship" intact. Julia accuses Barbie of cheating on her with Eva, which upsets him and causes him to leave. Eva learns that she is not in fact pregnant. Christine takes Junior to the tunnels and spreads some of the material/slime from the main pod onto his lips, then seduces him. Julia joins up with Big Jim and helps him flee from an Aktaion operative chasing him.

Big Jim and Julia learn some information about the egg from Dr. Marston, an Aktaion scientist. Hunter falls off a roof while trying to force Norrie to return to work, resulting in his legs becoming paralyzed. He later blames Norrie, causing Junior and some of the townspeople to become angry at both Joe and Norrie. Sam finds Abby dead after Christine gives her some pills. Barbie saves both Eva and himself by killing Pete after he is tricked by Christine into believing Barbie is a threat. Big Jim saves his dog, Indy, from Aktaion agents by telling them the truth about the egg and Dr. Marston then tells him that he will be used as the control and Christine will be used as the experiment.

Joe and Norrie learn about the infected town's new rules. They also find out that Carolyn is infected. Julia is kidnapped by Junior until Joe and Norrie rescue her. Barbie and Junior rescue Christine from Aktaion agents while Big Jim kills Dr. Marston and runs into the woods. Joe and Norrie later rescue Hunter and due to Christine killing Abby, Sam stabs her; although not killing her. Big Jim walks around the woods in search for his dog, Indy, and finds Julia as they both team up and walk together in search for Indy, knowing that most of the town is infected.

The residents of Chester's Mill watch on helplessly as the world around the Dome is struck by a meteor shower and the ejecta. Barbie and Eva deal with members of the Kinship attempting to jump from a building due to Christine's absence, and Barbie suggests to Eva that they send a signal from Bird Island to bring survivors inside the Dome. At the diner, Joe and Norrie help Hunter return to his old self when they learn that emotions can help fight against the Kinship. Meanwhile, Big Jim and Julia bond and get drunk at the Aktaion house on Bird Island and discuss their regrets, and the end of the world. Junior lures Sam into the caves by telling him about Christine and pretending not to know he attacked her, he then attacks Sam while inside. Christine later starts to reemerge from her cocoon. Barbie despairs as he watches on at the Dome wall as survivors are enveloped by the firestorm. Eva tells him to forget about them, and convinces him to join the Kinship. Joe, Norrie, and Hunter join Big Jim and Julia and form a resistance. A voice is heard from the computer inside the house, indicating that not everyone outside the dome has perished.

The destruction seen outside the Dome turns out to be an illusion. Christine convinces the townspeople to begin mining the remaining crystals powering the Dome and bring them to the surface, where they will be more effective. Hunter and Big Jim communicate with Aktaion via the computer and offer to exchange Dr. Marston for a load of explosives. Big Jim places the explosives near the crystals. Barbie finds them and warns the townspeople to evacuate the mine, but they explode and Norrie's mother, Carolyn, is trapped and apparently killed. Now lacking power, the Dome begins to calcify, which will eventually cause the townspeople to suffocate.

The Resistance escapes to Reverend Coggins' funeral home after the Kinship invades the Aktaion house. Joe and Norrie are chased by the Kinship at the library, but Sam saves them and is presumably on their side. Julia and Big Jim capture and interrogate Barbie, hoping they can snap him out of it. When it doesn't work, Big Jim attacks Eva and the Kinship, but after a brief struggle, he escapes. Back at the funeral home, Sam knocks Joe out and takes him back to City Hall, revealing Sam is part of the Kinship. Julia confronts Barbie alone at gunpoint, threatening to shoot him. However, Julia expresses her love for Barbie, which snaps him out of it and the two share a kiss together.

After Barbie and Julia share a romantic kiss together, they make plans to get the town out of the Kinship. Big Jim, Norrie, and Hunter fight off the Kinship and get rescued by Hector who had just gotten inside the Dome alongside his Aktaion crew. Barbie finds Junior punching Joe at the town hall and tells Junior to leave. Barbie tells Joe that Julia freed him from the Kinship and Joe decided to stay and help plan on bringing down the Dome. Julia and Indy meet up with the Resistance and the Aktaion crew. After being threatened by Hektor, Big Jim begins to fear that he will end up betraying them. Julia finds several dead bodies of young women until Harriet finds her. Norrie shoots Harriet through the head and they both watch as Barbie holds hands and kisses Eva.

Joe continues his research on using sound to bring down the Dome. He learns that the crystals respond when people whistle the tune, but not when a recording is played. He splits the one big crystal into seven pieces. The Aktaion team develops a possible cure for the infection, which is tested on Junior. Eva has the baby. Eva's usefulness is done and she is killed by Christine, who takes the baby. Big Jim agrees with Hektor when he says that killing the infected townspeople is the only way to stop the Kinship. Joe wonders what will happen if the Dome comes down while the townspeople are still infected, led by their new Queen.

Barbie and Julia return to the Resistance, where they inform them of Barbie's daughter being part of the Kinship. Dr. Bloom insists on them getting the baby's umbilical cord to create a new cure for the infected townspeople. Junior returns to Christine, who has placed Barbie's daughter in a cocoon and has started the process of turning her into the new queen. After Barbie and Julia give the umbilical cord to Big Jim, they interrupt the transferring process and a shadow figure escapes the cocoon and turns Christine into a normal person again. She takes them to the lake, where they manage to stop Junior from going through with Christine's initial plan to sacrifice the kids. Hektor, adamant that the cure will not work, kills Dr. Bloom and ties Lily up and goes to kill Joe. He is about to kill Joe and Norrie, but Big Jim intervenes and kills Hektor. Dawn, Barbie's now grown up daughter, kills Christine and declares herself as the new queen.

Sam advises Dawn that there are tunnels at the cement factory that lead out of town. Jealous of his position in the Kinship, Junior seeks to reclaim his position by killing Sam. The crystals are in place and the transmitter is ready. Dawn activates the crystals but the egg is required and is not available. Dawn tells Norrie that she can act as the egg since she is a Hand. Joe takes Norrie's place and the Dome comes down. Junior attacks Big Jim, who is forced to kill his own son. Dawn apparently falls to her death at the cement factory. Everyone is required to sign a statement that Hektor and Aktaion were responsible. Big Jim offers to fully sell the story if he is compensated "fairly". One year later, Barbie is about to propose to Julia when they are taken to Big Jim's office, who is now a Congressman. Hunter (who is now working for the NSA) has located Dawn in Omaha. Norrie (who has enlisted in the Army) finds Joe in a secure facility. Dawn stops three children before they touch a different egg.