Barbie, Sam, Pauline, Lyle and Hunter try to evade Don and his forces and find a way back to Chester's Mill, while Junior and Melanie hide the egg from Julia and Big Jim.
When Barbie enlists his father's help to reach out to Julia, he realizes that Don may know more about the Dome than he is letting on. Meanwhile, Big Jim appoints himself sheriff of Chester's Mill.
When Barbie descends into the unknown abyss in the mysterious tunnel to look for Sam, he discovers a world that is familiar but filled with unanswered questions.
When Barbie and Sam set out to investigate a mysterious tunnel, a cave-in severs their path back to Chester's Mill. Meanwhile, Julia and Big Jim face off in a struggle for power as a dust storm rages in the town.
Julia takes over as leader of Chester's Mill after the town becomes divided in the wake of Big Jim and Rebecca's plans for population control. Meanwhile, Joe and Norrie help Melanie search for more clues about her identity at the Dome wall.
As conditions in Chester's Mill worsen, Big Jim and Rebecca consider resorting to population control, which drives a wedge between Barbie and Julia. Meanwhile, clues to Melanie's past and her connection to the Dome are revealed.
When tensions in Chester's Mill continue to rise as resources dwindle, Big Jim holds a census in order to forecast how long the town can continue to exist under the dire conditions. Meanwhile, a rainstorm brings much-needed water until it changes to acid rain, threatening the lives of everyone it touches. Also, Rebecca and Lyle butt heads over the reasons for the dome's existence.
As Barbie's fate lies in Big Jim's hands, the dome presents a new threat when it becomes magnetized. Meanwhile, Julia seeks out the help of a stranger to save the life of a mysterious girl.
Julia awakens from her coma and insists that she and Angie free Barbie before they worry about the mini-dome and the black egg. Joe, Norrie and Junior watch the butterfly come out of the chrysalis but it appears trapped in the mini dome. As it flies around, the mini dome blackens as does the big dome, plunging Chester's Mills into darkness. Julia, Barbie and Angie catch up with them and find the mini dome disintegrated. The butterfly is alive however and the monarch is identified. While the monarch races to protect the egg, Barbie is recaptured and led to the gallows.
The entire town rallies to find Barbie after Big Jim convinces them he is behind the recent murders and shooting Julia. Barbie realizes that Julia's life is in danger - Jim's story will fall apart once she regains consciousness and tells people what really happened. Barbie and Angie hatch a plan to get her out of the clinic but Barbie soon finds himself in jail and Big Jim has a proposition for him. Joe and Norrie move the mini dome to Ben's house but it soon begins to act strangely.
Big Jim reports to the police station as promised and convinces Linda that his stash of propane is what's saving everyone today. He tells her the biggest threat they face is from Barbie. After spending the night on the couch, Barbie tells Julia he didn't like it much and she admits she didn't much like sleeping alone either. She answers a knock at the door and comes face to face with Maxine who promptly shoots her in the chest. Barbie races to get her to the hospital. Back at the barn, Joe thinks the stars are about them but Junior runs off after failing to convince Angie they should be together. After the shooting and Junior running off, the weather turns nasty. After it clears, Joe and the others head off to the dome and see something they wish they hadn't.
Maxine extends her reach in Chester's Mills by opening a bar where people can gamble on bare-knuckled fights. Big Jim pays a visit to a lake island home hoping to find the information Maxine has on him and Barbie. After Linda finds a safe-deposit box key in Duke's hat, she and Julia head off to the bank. Duke left some incriminating information. Julia checks her husband's box leading her to understand better what happened to her husband. Dodee finds the mini dome but is injured when she touches it. After speaking to a nurse at the hospital, Angie is certain she know the identity of the fourth hand.
Julia takes Barbie into the woods to show him the mini-dome but it has vanished. A search through the woods yields little information. After Barbie and Sheriff Esquivel arrest a drug user, they first hear of a new drug, rapture. Jim arrives home and finds Maxine, the head of the drug operation, waiting for him. She was in Chester's Mill the day the dome appeared and has been lying low ever since. It turns out Barbie knows her as well. Big Jim wants to disarm everyone in the town. Junior visits Angie at the diner but she collapses and says 'the pink stars are falling'. Angie starts to think Junior's comments about not being well may have some merit. When Joe, Angie and Norrie finally locate the mini-dome and the egg, they also realize the assistance of a fourth person will be required.
Norrie is grieving over her mom's death and Julia can't help but wonder at the seeming coincidence of the new birth and the death. Norrie blames Joe for taking her to the center of the dome which she believes is what killed her mom. Joe shows Julia the egg and it has a message for her when she touches it. Big Jim has it out with Junior over the shooting of Cliff Dundee. Sheriff Linda Esquivel also tells him off, saying that if they weren't so short-handed she would have fired him. Junior learns that his mother committed suicide. Food shortages are now of concern and Ollie Dinsmore makes it plain to Big Jim that the shortages, including access to his well, will continue until he is thrown out of office. Big Jim's attempt to take control of his land fails when Ollie shows up with a half-dozen men. Junior joins Ollie's army. Big Jim is ready to go to war but Barbie has a better idea.
Norrie and Joe go to the dome to see if they can figure out what powers they might have over it. Joe wonders if the dome might have a nucleus at its center. It the very middle of the area covered by the dome, they make a discovery. Julia's next door neighbor Harriet is expecting a baby very soon but when she goes into premature labor, she thinks the dome may have done something to her baby. She had a vision of her absent husband just before labor began. A healthy baby is born but tragedy soon follows. Big Jim lays down the law with Junior as regards Angie and throws him out of the house. He also tries to re-establish his authority in the town after he learns that Ollie has taken over his propane supply. The police try to track down the Dundee brothers who killed Rose at the diner.
The residents of Chester's Mills face a new crisis when the town's water tower is damaged and the lake is found to be polluted. Big Jim knows but water can be find but it's going to cost him dearly. As the townsfolk learn of the shortage, panic sets in and riots erupt. Angie manages to get away from Junior and makes her way to Rose's restaurant. In the middle of the riot however, it's up to Barbie to rescue her from the town bully. Norrie is determined to find her sick mother a supply of insulin. While she and and Joe are out searching, Julia and Doddee are trying to pinpoint a strange power source - and realize it's coming from Norrie and Joe.
Julia hears a TV broadcast and learns the military has set up a 10 mile quarantine zone around the dome. The residents of Chester's Mill receive visitors however - friends and family who can at least see them from the other side of the dome. Norrie has a surprise waiting for her. For others, the reunions are bittersweet. Barbie learns from one of the soldiers that the army is pulling out. Rev. Coggins thinks he's receiving messages from God but his hearing aid is playing a role. He keeps hearing the word MOAB which he thinks is a biblical reference. Barbie knows otherwise. Big Jim finds Angie in his old bomb shelter and frees her. Junior isn't finished with her yet.
The military units outside the dome are packing up, much to the consternation of many of the townsfolk. There is a much greater problem however when Linda falls sick, the first of many as an outbreak of meningitis spreads across the town. Julia continues to have her doubts about Barbie and visits a site he had marked on his map. She finds her husband Peter's car at DJ Phil's trailer but he says her husband sold it to him. DJ tells her about the cabin and when Junior tells her about meeting Barbie at a cabin, she's desperate to get there but having fallen ill, has to get out of the hospital. Angie, still a prisoner in the bomb shelter, faces rising water after a pipe bursts. Norrie and Joe realize they have a seizure when they touch.
Deputy Paul Randolph escapes from custody and Linda Esquivel sets out to find him. In the meantime, Big Jim Rennie puts together a posse together and recruits Barbie to help out. Angie suggests to Junior that they try getting under the dome through the old cement factory tunnels. Most of those tunnels were closed off but Junior sets off to see what he can find. Julia follows him. Julia continues to wonder what the odds are of Barbie just being in town when the dome appears. Carolyn is worried about her daughter Norrie who was away all night. Norrie spent the night at Joe's house but when Caroline finds her both Joe and Norrie have a seizure. Junior begins spreading rumors that Barbie is a psychopath who attacked him for no reason.