In the city of Excelsior in California, Executive Prophet Donald Pynchon is walking down a street, passing a homeless woman. Everything around Pynchon suddenly goes silent and a man comes up behind the prophet and first cuts him across the legs and then stabs him to death. The nearby pedestrians don't hear Pynchon's silenced cries of pain.
The next day, detectives Caolan Longstreet and Jeff Bosson are called to Pynchon's murder scene. They secure the area and confirm there was a struggle, and Longstreet attempts a spell to raise the blood and then "play it back" to follow how it was spilled. When he starts to lose control, Bosson takes control of the spell. As Longstreet casts a spell to capture images of the blood, Bosson "rewinds" the blood and determines that Pynchon was hamstrung and then stabbed in the kidneys. The killer then watched as the dying Pynchon tried to crawl away.
Necromancer Dr. Morgana Kurlansky arrives as the detectives confirm Pynchon's identity and call in their superior, Detective Inspector Wilder Blanks. Kurlansky speaks with Pynchon's spirit who refuses to discuss who killed him, merely saying that it's a matter of vengeance. Kurlansky warns that the injustice will follow him into the next life but Pynchon simply walks away.
When Wilder arrives, forensic officer Andres Lopez reports that he's found a charm of silence on a nearby lamppost. The charm explains why no one heard Pynchon's dying screams. Lopez is able to identify the charm as having come from Mendocino. Wilder tells the detectives to keep him informed and returns to the 17th precinct house. As he reads a newspaper article about Pynchon's death, Wilder suddenly gets a vision of someone warning against the return of an old foe. The inspector sees an image of some kind of elaborate mechanical device shooting out a projectile. The deputy inspector, Liam Butterfield, comes in and tells Wilder about the other open cases. However, Wilder tells him to put a hold on the other investigations and then tells a surprised Butterfield that Detective Mira Barkley will be arriving shortly.
Mira is in Excelsior Superior Court watching as Judge Leslie Harowan decides to sentence the defendant that Mira brought in to the dislocation of his right arm for one year. The detective complains that the sentence is too late and that the man is a member of a gang that has been terrorizing the area, but Harowan stands by her decision. After the court adjourns, Wilder approaches Mira and tells her that the stoics are back. They go to lunch and Wilder tells her that he's been basing his guess on a hunch and his earlier vision. However, they both know about the stoics from 12 years ago and Wilder says that he wants Mira out of Robbery and back into Homicide when more bodies turn up. Mira isn't interested but Wilder reminds her how dangerous the Stoics are and the detective reluctantly agrees. Wilder admits that he already cleared her for duty and then tells her that she'll be working much to her partner despite her objections.
When Mira arrives at the station, she confronts Butterfield and calls him "Lisa" rather than "Liam." Butterfield insists that he's Liam now and takes her to see her new partner, Jimmy Travers. Jimmy is at the firing range practicing with an amulet. He almost hits them when he swings around and Butterfield hastily tells him to holster his weapon. He then introduces Jimmy to Mira, enjoying the fact that Mira is stuck with a rookie partner. He gives them the case file on their first assignment and Mira is disgusted to learn that it involves a hexed apartment building in Telegraph Hill. When she objects, Butterfield tells her that he doesn't know why Wilder brought her back but that for the time being he'll be the one assigning her cases.
As Mira and James drive to the apartment, James tries to make small talk but his new partner sticks to covering the basics. She figures that James is a hot new rookie and Wilder wants her to break him in. Once she's done, Jimmy will get a new partner. When they arrive at the apartment building, they discover that all the doors and windows are opening and closing on their own. They talk to the landlord, Delmore Keaton, who demands that the city take care of it because it's a curse. Mira examines the wall of ivy in his office that provides some of the power for the building and discovers that it's covered with beetles that feed on active magical energy. She tells Jimmy and Delmore that someone is using an onyx totem to redirect the ivy's magical energies to power the poltergeist activities. The detectives order Delmore to have the residents shut down all of their plants so that they can track down the totem.
Bosson goes to see Pynchon's wife, who remembers that her husband was arguing with someone over the phone on the day before he died. She explains that Pynchon had cast his annual prophecy for the Equinox and saw something that disturbed him. He called Deputy Mayor Ben Cole and they argued, and her husband refused to let Cole harass her. Bosson and his partner then go to see Cole, who admits that he saw Pynchon the morning of the murder. However, he insists that he had nothing to do with the Executive Prophet's death but they ask for his alibi. Cole tells them that he was out drinking with friends, passed out, and they took him home. When they push for the name of the friends, Cole finally admits that he was with his mistress and she was the one who took him home.
Bosson and Longstreet visit Samantha and her son Leo lets them in. She confirms that Cole was drinking, stopped by, and passed out. After that, she called a cab and sent him home. However, the detectives realize that she's describing it almost word-for-word the way that Cole did. They also notices that she's taking medicine for allergies, medicine that could also cover dermal bruising. Bosson casts a spell revealing that she has bruises on her face and Samantha admits that Cole became violently drunk and beat her before he left. The next day Cole called her back and told her to keep the jacket that he left there until he sent for it. Longstreet checks out the jacket and finds Pynchon's Equinox prophecy in the pocket. According to the prophecy, someone in the mayor's inner circle would be revealed as an embezzler in the coming year.
That night, Delmore finishes having all of the tenants shut down their plants except one. He tells the detectives that she was worried about turning off her cat's litterbox vaporizer. They finally locate the onyx totem in the basement and Jimmy removes it using a pair of forceps. As he secures it, he has a vision of a strange mechanical device, the same one that Blanks saw in his vision. He tells Mira that something is wrong and runs upstairs to one of the apartments. Delmore tells Mira and Jimmy that the apartment belongs to the woman who objected earlier, a Professor Lana Keystone. The professor doesn't answer when they knock and the detectives break in. Keystone is lying on the kitchen floor, dead.
Once the detectives call in the murder, Kurlansky and Wilder arrive at the crime scene. Keystone's spirit refuses to say anything to Kurlansky and will only keep asking about her sister. Mira checks Keystone's background and learns that she was an expert on magical power plant design. Kurlansky is unable to confirm what killed Keystone and can only confirm that it was some kind of unidentified physical trauma. As the necromancer prepares to fast to conduct the necropsy, Mira asks Wilder why he didn't tell her that Jimmy is an intuitive savant. He admits that he didn't know for sure but assigned Jimmy to her because she had worked with one in the past. Jimmy checks the apartment and discovers that Keystone had dozens of protective charms hidden in the kitchen cupboard. Mira remembers that Delmore mentioned that Keystone didn't want to shut down her power plant and they realize that she wanted to maintain the power to her charms. The detectives figure that the killer planted the totem to force Keystone to shut down her charms so he could get to her. Jimmy warns them that the murders are just beginning and then wonders how he knew that.
The next day, Bosson and Longstreet bring Cole in for interrogation. Bosson says that they found the prophecy in his jacket pocket but Cole claims that it was fake. However, when Bosson says that they know Pynchon delivered the real one to him and threatens to call the press and reveal that Cole beat Samantha, the deputy mayor caves. He admits that he destroyed Pynchon's prophecy because it would have panicked the city. Pynchon had predicted that an old foe was returning and that the coming year would bring darkness and death. Butterfield and Longstreet watch Cole through a one-way magical wall as Cole claims that Samantha attacked him when he refused to move back to Mendocino with her and abandon his wife.
Back in the precinct room, the detectives go over the evidence and Longstreet remembers that the silence charm came from Mendocino. Butterfield confirms that Samantha rented a house in Mendocino two and a half years ago despite the fact she had no source of income. She and Leo left two years ago and came to Excelsior, but there's no record of her prior to two and a half years ago. Judge Ball at the superior court in Mendocino issued her an ID and closed her file. Andres reports that the of the charm matches that of a child and the detectives figure that Leo must have drawn it.
The detectives bring in Kurlansky, who admits that the wounds had to have been caused by a short person. However, Basson notes that the pattern of the blood suggests that the murder took sadistic pleasure in watching Pynchon crawl, which doesn't match with a child's psychology. Kurlansky suggests that Samantha may have used her son as a murder weapon by applying sympathetic magic. Longstreet makes a call and confirms that the Shetlands have left town, suggesting guilt. However, Wilder points out that they have no motive for Samantha to kill Pynchon. They check the records and discover that Pynchon traveled on lecture tours and was in Mendocino at the same time as Samantha. However, half of the article about his lecture is missing. Butterfield theorizes that Judge Ball cast a record to blank out the records and protect Samantha's history. Since then, Ball has retired and doesn't take calls. Bosson and Longstreet leave with Wilder to visit Ball and get the full story.
That night, the three officers arrive at Ball's house and discover that someone has cast an anti-sound charm like the one at Pynchon's murder scene. They split up and enter the house from three different sides. Unaware that Samantha is behind him, Wilder enters the study and the woman throws a knife at him. He manages to duck it at the last minutes and opens fire on her, and she runs upstairs into the house.
Ball pulls up to the house and discovers that someone has cut the magical power to the house. Leo attacks her with a knife just as Longstreet reactivates the magic plants and deactivates the silence charm. He hears Ball screaming and runs to investigate. Upstairs, Wilder manages to ambush Samantha and shoots her, knocking her off the balcony. She falls to her death while Longstreet restrains Leo. Ball arrives and tells them that Leo's real name is Lionel Dixon... and he's 42 years old.
Once the officers secure the scene, Ball tells them that in 1996, Pynchon had a vision of a murder and picked the 42-year-old Lionel out of a lineup. Lionel was convicted and given a life sentence, and Ball forced him to magically relieve the dying memories of the victim twelve times a day, every day of his sentence. However, two years ago there was a similar murder and they caught the killer in the act. He confessed to the murders in 1996 and they realized that Pynchon had mistakenly identified Lionel in 1996. Ball cast a rejuvenation spell on Lionel to restore him to his 10-year-old age as a means of recompense. "Samantha" was actually Catherine Dixon, Lionel's sister. Ball gave her a new identity and sealed her history file so that she could pose as Lionel's mother and the two of them could start a new life together.
Later, Wilder returns home where his girlfriend Kurlansky is waiting for him. He tells her that Harowan will try Lionel and offer him a deal: he can go free if he agrees to a new spell turning him into a 90-year-old. Wilder is worried that just like Pynchon relied on his intuition to testify against Lionel, he has also gone after several criminals based on nothing but intuition. Kurlansky assures him that she trusts him and then asks if he read her report on the murder weapon in the Keystone case. She says that she's never heard of a weapon like the one that was used and Wilder tells her that he has.
Mira takes Jimmy to a bar to drink and he explains that he became a cop based on a random whim. She warns him that nothing is random and starts to tell him about a group known as the Stoics.
Wilder tells Kurlansky that the Stoics are responsible for Keystone's death, and that the group is dedicated to the destruction of magic. They believe that the judicial system is subject to hunches and irrational emotions rather than rationality and logic. They want a world based on something that they call "science." Pynchon was wrong about Leo but right about his prophecy. Because he was overwhelmed by such a powerful vision of the future, he was unable to see his own death.
Mira tells Jimmy that the Stoics are terrorists will do whatever it takes to destroy the world as it exists and rebuild it in their image. The police have no defense against "science" and the weapons that they used are something called "guns." She shows Jimmy the small metal object that was used to kill Keystone and tells him that it's an item known as a "bullet."