Two weeks ago, a bloodied Luke Chalfant is hanging under a tree. He is being held captive by Jerathmiel, a witch hunter from the Order of the Innocents who tells him that his namesake Luke the Apostle was hung upside down from an olive tree. The witch-hunter says he doesn't want to hurt him but to save his soul. Luke denies that he knows anything about the witches of Greendale, but Jerathmiel does not believe him. Jerathmiel already knows that his coven is the Church of Night and that his High Priest is Faustus Blackwood. He knows that Father Blackwood sent him on a mission and demands that he give the names of his fellow witches and the location of where they meet. Luke tells him that the witches and warlocks meet in the woods, a school, the Academy of Unseen Arts. The witch-hunter is excited at the prospect of a whole academy to evangelize to. However, Luke responds that only the hands of the initiated can open the doors of the Academy. The witch-hunter mockingly tells him that he brought him two before proceeding to cut off Luke's hands and kill him.
Present day, several days have passed since Zelda and Father Blackwood left for their honeymoon. Sabrina tries to enter the Academy, but her hands are burnt due to her expulsion. She bangs on the gate. Prudence opens the door and reminds Sabrina of her expulsion. Sabrina demands to see her cousin Ambrose. Prudence refuses because Ambrose allegedly murdered the Anti-Pope and tried to kill her father. Sabrina believes Ambrose is innocent. Sabrina appeals to Prudence as a friend, but Prudence counters that Sabrina only uses her and the Weird Sisters. Sabrina reminds Prudence that she saved her life at the Feast of Feasts, but Prudence counters she had selfish motives and that they were merely allies of convenience.
After Prudence closes the door, Sabrina is greeted by Quentin, who tells her that Ambrose is imprisoned in the Witch's Cell. Quentin tells her that the Weird Sisters are planning to torture Ambrose.
Sabrina brings this news to Hilda, who says she has tried contacting Zelda by a witch-board. Sabrina wants to lodge a complaint with the Council. Hilda says that they will have to summon the Trivium there and expresses her concerns about Ambrose's well-being.
Ambrose is working out in his cell when Dorcas enters with his gruel rations. Ambrose requests something more succulent and rubs his body against Dorcas. Prudence tells Ambrose to get away from her sister, shoving Dorcas to the ground and her to drop the tray of gruel. She chides Dorcas for her infatuation with Ambrose. Ambrose tries to flirt with Prudence, but she denounces him as a traitor and tells him that he will rot in this cell until he provides a confession. Ambrose says he has spent 75 years under house arrest and that it will take more to break him. Prudence allows the Infernal Bailiff to rough Ambrose up.
Sabrina and Hilda summon the Trivium and appeal on Ambrose's behalf. The Trivium tell her that they have consulted with Father Blackwood and decided there will be no trial. They announce that Ambrose will be executed on the day that Father Blackwood returns from the Necropolis. Sabrina says that Ambrose is innocent, but the Trivium say that the coven witnessed his murderous acts and warn Sabrina not to summon them again or she will be held in contempt.
At the cottage, Adam tries to convince Lilith, whom he still assumes to be his lover Mary Wardwell, to spend the day with him. She claims that she has her duties as a principal. Adam says she is underappreciated and pleads with her to go on holiday with him. She says she has to make arrangements at Baxter High before spending the rest of the day with him.
Back at the Spellman household, Sabrina tells Hilda that Nicholas is drowning his sorrows at Dorian's Gray Room. Sabrina wishes Zelda and Ambrose were there. Hilda vows to break him out of his cell. Since she is no longer excommunicated, Hilda proposes bribing her way into the Academy with a delicious roast chicken. Sabrina tells Hilda that she plans to visit Principal Wardwell at Baxter High to seek her help. Hilda thinks it will be good for Sabrina to meet up with her mortal friends.
At Baxter High, Theo delivers a presentation about the Children's Crusade in 13th century Europe. He explains that as the children paraded through Europe, they offered each soul the choice of pledging their faith and joining the mission or burn in the fires of Hell. After class, Sabrina chats with Theo and Harvey in the corridor and asks about Roz. Harvey says that he has to go to the gym. Theo tells Sabrina that Roz is going through a brutal time since she lost her sight.
Sabrina meets Rosalind in the library. When she asks why Roz did not tell her, Roz replies that Sabrina was not there. When she asks why they are keeping her in the library, Roz says it is better this way. Sabrina speaks to whom she believes to be Principal Wardwell, but is actually Lilith and tells her about her exclusion from the Academy. Lilith hopes things will work out. Before she leaves, Sabrina asks about Roz, who is angry at the world about the unfairness of the situation. Sabrina doesn't want Roz to be isolated in the library, and she should be allowed in classes. Lilith replies that studying in the library was Roz's choice. Sabrina simply wants to help her friend and Lilith suggests giving her a comfort charm or even using a spell to restore Roz's sight.
Sabrina gives Rosalind a comfort charm, but Roz accuses Sabrina of only trying to comfort herself. A bitter Harvey, who clearly isn't happy Sabrina moved so far and fast on from their break up, says that not everyone can leave whenever they want and come back whenever they want. Sabrina offers to heal Roz with a spell, but Harvey objects to it due to what happened with his brother Tommy. Sabrina angrily tells Harvey that it is Roz's decision not his, silencing him. Roz turns her down by stating how distrusts witches since witches cursed her ancestors with blindness. She also asks if it was a coincidence that she went blind after she kissed Harvey, who is Sabrina's former boyfriend. Sabrina denies that she hexed Roz. Although, with both Roz and Harvey accusing her, Sabrina storms out. As she runs through the hallway, Jerathmiel notices her.
Prudence refuses to let Hilda bring a plump chicken for Ambrose. Hilda offers the chicken to Prudence and the Weird Sisters in exchange for allowing her to visit Ambrose. But Prudence says her father won't allow it. Hilda implores Prudence to let her visit Ambrose, but she remains impassive.
Back at Baxter High, Theo asks Rosalind and Harvey where Sabrina is. Roz hatefully replies that she left again. When Theo asks why, Harvey venomously replies it's because they couldn't trust her. Roz says that witches cursed her family and that Sabrina may have made her blind. Theo speaks out for Sabrina and says that she is their friend and a good person. Harvey tells Theo to name one good thing Sabrina's done. Theo reminds Harvey she saved the town to which he retorts "from witches." Theo also reveals that Sabrina got him on the basketball team and points out that Sabrina stopped Harvey’s father from drinking himself to death. This makes Roz regret what she said to Sabrina and makes Harvey finally realize that he's been being a jerk to Sabrina and that that's why she moved on so fast.
At the Academy, Prudence allows Hilda to spend time with "Ambrose" in Father Blackwood's office. Hilda hugs "Ambrose" and asks how he is doing. "Ambrose" reassures her that he is okay and claims they are treating him well given the horrible things he has done. Meanwhile, Prudence leads "Hilda" into Ambrose's cell. Ambrose asks if it is really her and she comforts him. He says that death would be much better than a living hell. "Hilda" tells Ambrose to plead guilty. Back in the Blackwood's office, "Ambrose" offers to plead guilty and tells Hilda not to give his plight another thought, however, Hilda is certain of his innocence even as Amobrse admits to the murder.
Back in the cell, "Hilda" tells Ambrose to plead guilty despite his denials. However, Ambrose insists that he's innocent. In the office, Hilda recounts a party they held to celebrate the passing of old Vinegar Tom. "Ambrose" says he thinks about it often, but Hilda points out that Vinegar Tom died in 1989 on the day that the Berlin Wall fell. Hilda realizes that she is talking to Agatha, who takes off the glamour as "Ambrose". Back in the cell, Ambrose asks "Hilda" what is her favorite episode of Fawlty Towers. "Hilda" claims that she loves them all, but Ambrose points out that she hates Fawlty Towers and demands to know who she really is. Dorcas removes the glamour and tells him that he is going to die in the cell.
Sabrina visits Dorian's Gray Room where she finds Nick drinking his sorrows away. Nick is bitter because he regarded the Academy as his home. He says that Sabrina can always run back to her mortal friends, school, and boyfriend, which she tried to do, but failed. Nick blames Sabrina who decides to return home until he has "dried up."
Lilith walks with Adam in a park. Adam asks her if she would consider accompanying him to Tibet for a Physicians without Frontiers posting. He says he would not consider taking it unless she wants to come along. Lilith says she will consider it and let him know tonight. While standing by the bridge, Adam asks Lilith to make a wish. She throws a pebble into the river.
Prudence, Dorcas, and Agatha torment Ambrose by throwing him the bones from Hilda's succulent chicken. While going through the bones, Ambrose finds that one of the bones has a hidden key.
Jerathmiel visits Sabrina's home, identifying himself as a missionary. Sabrina tells him that she has a faith. Jerathmiel manages to convince Sabrina to offer him a glass of water. Salem growls at Jerathmiel. Inside, Sabrina asks Jerathmiel, who tells her to call him Jerry, if he gets many converts. Jerathmiel asks Sabrina what her faith is. Sabrina says she is a spiritualist and gives vague answers. He wonders if it comforts her. She honestly answers that it scares her. Sabrina asks Jerathmiel what is at the heart of his religion. Jerry replies that it is forgiveness and salvation. When Sabrina asks if some people are beyond saving, he claims that nobody is beyond saving.
Meanwhile, Harvey and Rosalind are working on an assignment on the Children's Crusade when Roz experiences a premonition of Jerathmiel killing Sabrina. Roz tells Harvey to give her the phone.
Sabrina is having a conversation with Jerathmiel about sin. Jerry reassures her that any sin can be washed away so long as she ask for forgiveness, but Sabrina is skeptical. Just then, Sabrina's phone rings. Rosalind warns Sabrina that the missionary wants to kill her and tells her to flee. Sabrina catches a glimpse of Jerathmiel wielding a knife and flees out of the house. She manages to lock him inside with a spell, but he forces his way out. Sabrina fleets on her bicycle with Salem.
At Cerberus Books, Hilda tells Dr. Cerberus about her plan to help Ambrose escape by tricking the Weird Sisters into throwing the bones at him, allowing him to make a skeleton key. A female witch-hunter named Mehitable enters the store and tells Hilda to repent and beg the Almighty for forgiveness. When Hilda refuses, Mehitable replies that Hilda and her witch kind can perish in hell. She unsheathes a knife. Hilda kisses Dr. Cerberus, setting his incubus free. Dr. Cerberus roars and attacks.
At Dorian's Gray Room, Nick insists on drinking himself to death since he has nothing to live for. Dorian is struck in the neck by an arrow. An armed witch-hunter named Gideon sporting a crossbow says that he has come to destroy Dorian Gray. He offers Nick the chance to repent. Nick tries to teleport, but is too drunk to remember the incantation. The missionary is about to fire another arrow at Nick when a bloodied Dorian Gray surprises him and stabs him through the chest with an arrow. Dorian Gray says he has a particular invulnerability which makes him insanely difficult to kill. Nick convinces Dorian not to kill Gideon until he tells them everything.
Sabrina finds Hilda in the damaged Cerberus Books. Hilda reassures her that they are safe and that Cerberus chased the witch-hunter away. Sabrina says that she was attacked by a male witch-hunter, meaning there are two of them, but Nick tells her that there are three. He explains that the witch-hunters are from the Order of the Innocents and that the one who stormed Dorian's Gray Room has been trapped inside a painting. He hugs Sabrina and apologizes for his behavior. Nick explains that the Order of Innocents want to kill all the witches in Greendale, starting with the outliers before converging at the Academy. Sabrina says they have to warn them, but they've been expelled and can't enter the Academy without a Hand of Glory. Hilda says she has gotten a dozen.
Lilith is having dinner with Adam and compliments his cooking skills. When she asks what is for dessert, he replies that dessert is her reward for saying yes to Tibet. Lilith points out that she has not said yes yet, but Adam reiterates his request that she goes. Lilith acquiesces and then spits out a ring. The Dark Lord appears and reveals that he has killed Adam, serving his head as dessert. He reminds Lilith that their bond is eternal and that there is no escape to Tibet. He orders Lilith to eat Adam's head, distressing her.
Back at the Academy of Unseen Arts, the Weird Sisters have gathered the students. With their help, Prudence, Agatha, and Dorcas tell the students that tonight they are collecting their energies to enact a spell of compulsion. She enlists their help on forcing Ambrose to confess to the murder of the Anti-Pope. The witches and warlocks begin chanting in unison. Meanwhile, Ambrose uses Aunt Hilda's bone to forge a skeleton key to unlock the door to his cell. As they chant, he runs out of his cell.
The two remaining witch-hunters, Jerathmiel and Mehitable converge on the Academy. Jerathmiel uses Luke's hands to unlock the door. The two of them encounter Ambrose, who warns the Academy that witch-hunters have arrived. Prudence orders the other witches and warlocks to hide while she and the Weird Sisters face the intruders. Jerathmiel and Mehitable enter the lobby and demand that the witches and warlocks come out of hiding.
Prudence, Agatha, and Dorcas emerge from hiding and use magic to force the two witch-hunters to their knees. She tells Jerathmiel that the pain in his head is his brain atomizing into sand and Mehitable that the pain in her chest are her lungs hardening. The Weird Sisters tell the witch-hunters that they are no ordinary witches but they are the daughters of the Church of Night, the "Three-In-One." However, Mehitable and Jerathmiel call upon the Heavenly Choir of the Nine Principalities to give them victory over the witches, causing the Weird Sisters to bleed from their eyes and ears. Mehitable and Jerathmiel tell them that they are no ordinary witch-hunters, but they are angels.
Sabrina, Hilda, and Nick are about to leave for the Academy with the Hand of Glory when Harvey arrives with a loaded rifle. Harvey tells her that Roz had a vision that someone was trying to kill Sabrina and he had come to check if she was safe. Harvey apologizes for his and Roz' behavior. Sabrina tells Harvey that the Academy is under attack and he offers to help. Nick does not want Harvey to come along since he distrusts him for coming from a family of witch-hunters. Harvey tells them that they need all the help they can get. Hilda backs Harvey up and they allow him to come.
Lilith sobs over the death of Adam and asks how the Dark Lord discovered them. She says that the ring should have hidden Adam. Stolas caws, and Lilith realizes that it was him who reported to the Dark Lord. She realizes that Stolas has been reporting back to the Dark Lord and burns him to death with her mouth. Lilith vows revenge against the Dark Lord for killing Adam, saying that he is not omniscient and omnipotent.
Sabrina, Hilda, Nick, and Harvey discover that the witch-hunters have breached the Academy. Sabrina calls for the Weird Sisters. She and Hilda find a bloodied Ambrose, who has been stabbed and is losing a lot of blood. Hilda removes the knife and casts a spell to seal the wound. Ambrose says that the Angels took the others. Harvey asks aren't angels supposed to be nice, but Nick points out that they have fiery swords. Quentin appears and tells Sabrina that the Angels tried to take him and the other children to Heaven but that they ran and hid. Hilda asks where the Angels took the other witches and warlocks. Quentin says that they took them to the desecrated church. When Harvey asks why, Nick explains that the Angels want to convert and kill them in order to cleanse them.
Quentin tells them not to go to the desecrated church because the Angels have sealed it with holy water and re-consecrated it. Quentin says that no witches can go in and out. Sabrina sends Quentin to hide. Hilda says that she has to tend to Ambrose's wounds. Harvey offers to go inside the church but Nick points out that they are dealing with avenging angels. Sabrina says that she can enter the church because she was baptized with holy water. Sabrina convinces them to accept her plan even though Nick and Harvey regard it as a suicide mission. She tells them to help Hilda look after Ambrose.
Jerathmiel and Mehitable tells the captive witches and warlocks that the stain of Lucifer blackens their souls. Prudence, Dorcas, and Agatha, are tied up and are to be burned at the stake. He tells them that God will forgive their sins if they vow to accept Him as their Savior. He adds that their bodies will be consumed and purified by the fire of righteousness. Jerathmiel starts with Elspeth, but she refuses to renounce the Dark Lord. Jerathmiel slits her throat. He then turns his attention to Melvin. As Melvin chants the prayer, his face begins to burn, causing him to collapse and vomit blood. Melvin is unable to continue with the prayer and Jerathmiel prepares to strike him down. Sabrina storms the church and orders them to stop. However, Jerathmiel shoots her with an arrow and demands that she kneels before the Lord. She refuses to submit and tries to call down fire.
However, Mehitable places a crown of thorns on her head, which prevents her from casting spells. Sabrina pleads with the angels to let them go as Jerathmiel shoots her with several arrows. Jerathmiel demands that she kneel and pray with them. Sabrina refuses. Jerathmiel then fires a third arrow at Sabrina in the heart, causing her to fall to the ground. Prudence, Agatha, and Dorcas are distraught. Blood gushes out of Sabrina’s wounds. Mehitable steps past Sabrina. Jerathmiel continues with his prayer, but Melvin chooses to die over pledging allegiance to the "False God." Jerathmiel then slices his throat, causing Dorcas to scream in grief. Jerathmiel is about to burn the Weird Sisters when Sabrina tells them "That's enough!" Everybody turns to find a reanimated Sabrina levitating in the church. She demands that the witch-hunters convert to Lucifer's faith or die.
Jerathmiel is defiant, but Sabrina summons fire with her hands and forces Jerathmiel and Mehitable to their knees. Seeking to save themselves, the witch-hunters chant the prayer to Satan. After Jerathmiel and Mehitable have uttered the prayer, Sabrina mocks them by telling them "Well done!" before noting how quick they were in turning on their "False God." When Jerathmiel demands to know what she is, Sabrina responds that she is the Dark Lord’s Sword before burning them alive in the presence of the other witches and warlocks. Sabrina uses her powers to resurrect Elspeth and Melvin from the dead. The Weird Sisters smile triumphantly as Sabrina hovers victoriously over the fallen angels. Harvey enters the desecrated church. Sabrina turns to face him, with her eyes a pale white.