While the Tiffany doll holds him at gunpoint inside the truck of Good Guy dolls he stole, Andy drives it off a cliff. Six months later, Jake now lives with a foster family in Salem, New Jersey, with his younger foster brother Gary. Both Jake and Devon suddenly receive threatening phone calls from Chucky, who reveals he is outside Lexy's house. Caroline lets him in, believing he is a trick-or-treater. Devon calls the police, but Chucky is already gone. Mayor Cross, attending therapy with Caroline and Lexy, blames the Hackensack murders on Junior. Their therapist, Dr. Mixter, helps Caroline overcome her new fear of dolls by giving her a "non-possessed" doll of her own, which resembles the original bride design of the Tiffany doll. Lexy grows suspicious and warns Caroline not to trust her or any other doll. Lexy alerts Jake and Devon of the new doll; they arrive at her house and stay the night. The next day, Gary arrives at Lexy's house with Chucky in tow. Carrying a homemade bomb, Chucky explains that his army of dolls survived the truck crash, and that he planned to lure Jake, Devon, and Lexy to the same location so he could kill all three of them. When Chucky is distracted, Devon tases him, causing him to drop the bomb. Gary picks up the bomb and runs, but Chucky attacks him and detonates the bomb, killing himself and Gary. Jake, Devon, and Lexy are blamed for Gary's death and, in lieu of juvenile prison, they are sent to the Catholic School of the Incarnate Lord. When they arrive, Devon immediately recognizes the school as the same building that contained the boarding home where Charles Lee Ray grew up. Shortly after their arrival, a mail truck delivers a Chucky-box-sized package to the school.

Tiffany wakes up next to the bloody head of the Tiffany doll that Andy killed. Nica-Chucky, who has now been Tiffany's captive for a year, says it's a warning that he is coming to kill her. A detective later visits Tiffany, investigating Nica's disappearance, but Tiffany kills him. At the School of the Incarnate Lord, Jake, Devon, and Lexy meet the headmaster, Father Bryce, as well as Lexy's eccentric roommate, Nadine, who admits she is a kleptomaniac. Lexy also discovers that Trevor, her childhood bully, is a student and altar boy. Meanwhile, the Chucky doll sent to the school awakens and causes a nun to die of a heart attack, whom he then photographs. When Father Bryce catches Jake confronting Chucky, he locks them in the same room. Chucky photographs Jake and escapes through the chimney. He then makes his way to Lexy's room and photographs her snorting clonazepam. Jake and Devon arrive and tie him up; Jake theorizes this specific Chucky is merely a scout for someone else. After it is revealed that Nica and Chucky have formed an alliance to take down Tiffany, Glen and Glenda, Chucky and Tiffany's twin children, arrive at their house.

Lexy discovers that Chucky has only one contact in his phone, named "The Colonel." Trevor, who sees the drugs in Lexy's possession, informs her that Mayor Cross lost re-election. He later threatens to use his leverage to ruin her life. When Chucky refuses to reveal any information, Jake instead attempts to sway him to their side by means of sensory overload and aversion therapy. It appears to work, turning Chucky docile (and, seemingly, amnesiac). Jake and Devon argue over their methods, with Devon wanting to kill Chucky, while Jake still overcome with guilt over Gary's death, believing he can only forgive himself if he can also forgive Chucky. Father Bryce witnesses the two kissing. Meanwhile, another Chucky doll is delivered to the school; he kills a priest while Nadine is in confessional. When Lexy suffers an anxiety attack, the docile Chucky leaves, later showing up on Father Bryce's desk. Lexy admits to Nadine that she suffers from depression and anger, and they grow closer. The next day, Trevor enters Lexy's empty room, but the newer Chucky follows him and brutally kills him. Jake, Devon, Lexy, and Nadine are forced to hide the body. The newer Chucky, who is bigger and stronger than normal, enters Father Bryce's office and threatens the docile Chucky.

Glen and Glenda, who believe Tiffany is actually Jennifer Tilly, question her about her knowledge of Nica; Tiffany feigns ignorance. Glenda then tells Tiffany of a recurring nightmare in which they murder a young woman. Glen and Glenda also reveal they've invited over Jennifer's friends and family - Gina Gershon, Joe Pantoliano, Sutton Stracke, and Meg Tilly - as part of a surprise party. Tiffany has also hired a butler, Jeeves, who quickly aggravates the guests with his crass questions despite Tiffany only hiring him to guard Nica's room. When Nica disappears from her room and Jeeves turns up dead, Tiffany pretends she's hosting a murder mystery party. As Tiffany searches for Nica and questions her guests about Jeeves's death, it is revealed that Glen is aiding Nica and attempting to help her escape. A flashback from three months ago further reveals that Glen and Glenda discovered a tied-up Nica, accidentally triggering an emergence of Nica-Chucky, who convinced Glenda to help him kill Tiffany. In the present, as Glen tries to usher Nica out of the house, the sight of Joe's corpse reawakens Nica-Chucky, and Glenda knocks Glen unconscious. With the aid of new metal arms, Nica-Chucky tries to shoot Tiffany, but the bullets are gone. Tiffany slaps Nica-Chucky, bringing back Nica; Glen elects to stay behind as Nica escapes with Glenda, entering a car driven by a still-alive Kyle. Finally, Chucky reveals to the audience that Glenda killed Jeeves, while Gina used up the gun's bullets, killing Joe.

The two Chuckys fight inside Father Bryce's office; the docile Chucky, now calling himself Good Chucky, gets the upper hand and incapacitates the evil Chucky via crucifixion. Nadine and Lexy discover that Trevor's body is gone. Devon becomes exasperated at Jake's continued defense of Good Chucky, who begins to doubt his own morality. The evil Chucky recovers in front of nun Sister Ruth, who is immediately convinced that he is a reincarnation of God. Meanwhile, Glen, who has been having the same nightmare as Glenda, confronts Tiffany about Nica's captivity, but Tiffany refuses to divulge any information unless Glen reveals Nica's whereabouts. When a suspicious Meg decides to stay at Tiffany's house, a captive Jennifer - trapped inside a Tiffany doll - feeds Tiffany false information, and Meg and Glen walk in on the two arguing. When Jennifer begs Meg for help, Tiffany murders Meg and reveals her true identity to Glen, bequeathing them the original Glen/Glenda doll. Tiffany and Glen burn down the house and leave with the doll and a tied-up Jennifer to find Glenda. Meanwhile, Devon and Lexy follow clues from the photos on Chucky's phone, leading them to a cabin near the grounds; in it, they see the bodies of Chucky's recent victims, "The Colonel", who is a bald Chucky torturing a still-alive Andy, and Dr. Mixter, who calls the doll "Charlie".

A flashback reveals that after the truck crash, several of the remaining Chuckys, including The Colonel, dragged an unconscious Andy to captivity. Dr. Mixter, who was Charles Lee Ray's childhood therapist, offers to help The Colonel kill the other teens. When they leave the cabin, Devon and Lexy free Andy, who demands they take him back to the school. Father Bryce, furious at Devon and Lexy for leaving the grounds, locks down the school. Devon and Lexy bring Andy (posing as a homeless man) to the school, and Father Bryce begrudgingly allows him to stay thanks to the influence of Sister Catherine. Meanwhile, Kyle convinces Nica to allow her to speak to Nica-Chucky, but he merely taunts her about Andy and unsuccessfully urges Glenda to kill her. Kyle, Nica, and Glenda later drive towards the school. Sister Ruth attempts to convince Father Bryce of the evil Chucky's God-like sentience, but he accuses her of heresy; The Colonel later kills the evil Chucky via arsenic-laced communion wafers. Sister Ruth vows to avenge him. Andy informs the teens that The Colonel went insane and killed all the other surviving Chuckys from the crash. He kills The Colonel but is disturbed to see Good Chucky. Dr. Mixter, armed with a gun, retrieves Good Chucky, locking Andy and the teens inside their room. Good Chucky sees Father Bryce and begs for help while Andy breaks down the door; in the ensuing chaos, Dr. Mixter wounds Sister Catherine and knocks Andy unconscious, while Good Chucky runs upstairs with Nadine in pursuit. When Nadine tries to comfort him, he briefly turns evil and pushes her out of a window to her death.

Dr. Mixter claims she needs Good Chucky, the final Good Guy doll, to free Nica-Chucky, who she calls "Chucky Prime." She forces Father Bryce, along with the rest of the group, to perform an exorcism on Good Chucky to send Chucky to Hell, in exchange for performing a voodoo ritual to move Chucky Prime to Good Chucky's body. A traumatized Lexy overdoses on clonazepam, causing her to hallucinate Nadine's ghost, who convinces her to keep going. Glenda demands answers from Chucky, but he simply calls them a killer and demands they help him escape. The exorcism causes Chucky to enter Father Bryce's body; Father Bryce then explodes. Nica successfully performs the ritual, and Jake attempts to kill Chucky Prime, but Sister Ruth arrives, holding Lexy at gunpoint. Jake allows Dr. Mixter to leave with Chucky Prime; Sister Ruth prepares to kill Lexy anyway, but Glenda kills Sister Ruth before she can. Andy chases Dr. Mixter and Chucky Prime; he kills Chucky Prime, but Dr. Mixter escapes. Meanwhile, with Jennifer Tilly now wanted for murder, Tiffany has formulated a new plan: to swap bodies with Jennifer again. However, Jennifer escapes from the car and is killed by an oncoming truck, devastating Tiffany. Tiffany and Glen arrive at the school, where Nica attempts to shoot Tiffany, but Glen jumps in the path of the bullet. Tiffany and Glenda take Glen away to get help.

A flashback reveals that Chucky Prime was able to perform the ritual to swap bodies with Dr. Mixter before Andy killed the doll. Now in her body, Chucky retrieves a new Good Guy doll from her office, which he transfers himself into (resulting in the police finding Dr. Mixter's body). With Glen's condition worsening, Glenda and Tiffany decide to save them by transferring them into the Glen/Glenda doll. After killing a suspicious cop, they perform the ritual - transferring both twins into the doll, now calling themselves G.G. Tiffany ships G.G. to England, so they can learn more about their origins. Weeks after returning home, Jake and Lexy enlist in group therapy, and Lexy invites Jake and Devon to stay at her house for Christmas. On Christmas Eve, Jake and Devon, along with Lexy and Mayor Cross, mend their respective relationships. Chucky arrives at the house, as does Tiffany, who is searching for Caroline's Belle doll. Chucky murders Mayor Cross when she comes down the stairs, and Tiffany doesn't intervene when Lexy arrives and kills Chucky. Jake and Devon wound Tiffany, but Caroline, whose mind has been fully twisted by Chucky, claims Tiffany is her real mother and leaves with her and the Belle doll. The next day, Jake, Devon, and Lexy are visited by Miss Fairchild, who believes their stories about Chucky. Three weeks later, after Tiffany and Caroline moved to New York, Tiffany received a threatening phone call from Nica (who is in New York as well), who swears revenge on her. Tiffany attempts to transfer her soul into the Belle doll but fails when it's revealed to be Chucky in disguise; he attacks Tiffany as Caroline smiles. Chucky then recaps the season's kills as he did in the first season.