1781 - Hudson Valley, New York
While the Americans and the British Redcoats fight each other, Professor Ichabod Crane is making his way through the battlefield. Whenever he finds a dead Redcoat, Ichabod checks their hand, looking for someone. As he searches, a huge figure of a man wearing the British uniform and a mask rides across the battlefield. Ichabod shoots him in the chest, knocking the man off of his steed, but the Horseman gets back to his feet and come at Ichabod with his broad axe. He knocks Ichabod's rifle out of his hands and Ichabod sees a brand of a bow on his opponent's hand. The Horseman cuts Ichabod across his chest, mortally wounding him, but Ichabod manages to draw his sword and decapitate the Horseman as he goes down. The two of them fall on the ground next to each other, their blood intermingling.
Sometime later, Ichabod wakes up and discovers that he has been buried in a cavern. Jars filled with animals around him shatter as he claws his way out of the ground. When Ichabod checks his chest, he discovers that his wound is gone. Staggering up a flight of stone stairs, Ichabod finds himself in the forest. He walks out past a small dam and finds himself on an asphalt road. As Ichabod tries to figure out what it is, a truck barrels by, almost running him over. A car comes by from the other direction, brushing him and going off the road. Startled, Ichabod runs off past a sign declaring that the town ahead is Sleepy Hollow.
That night, Sheriff August Corbin is at a diner eating with his partner, Lt. Abbie Mills. When Corbin rips out an article from the local newspaper and comments about the unsolved homicide, Abbie notes his interest in similar cases. The sheriff tells her not to worry about it since she'll be joining the FBI in a week, thanks to a feeder program. Nearby, Reverend Knapp watches them carefully. Corbin asks Abbie if she's running away from Sleepy Hollow but she avoids his question and goes out to the car. As Corbin walks after her, he nods to Knapp in greeting.
As they get to their police car, a call from in about a disturbance at the Ogleby Livery Stable. Abbie and Corbin drive out to the stable to investigate and split up. Corbin goes into the barn while Abbie checks the house. She spots Ogleby's truck nearby and finds a rifle on the ground... and Ogleby's decapitated corpse lying a few feet away.
As Abbie calls him, Corbin sees the figure of a Headless Horseman advances on him. He backs up against the barn door draws his gun and fires repeatedly, but the bullets have no effect. The Horseman decapitates Corbin with his broad axe, swing hard enough to pierce the barn door just as Abbie arrives. As she stars in shock, the Horseman smashes through the barn door, riding a white stallion. As it wheels around to face Abbie for a moment, she sees a bow-shaped brand on its hand. As it rides off, Abbie goes into the barn and sees Corbin on the floor, decapitated.
Lt. Andy Brooks is on patrol when he gets Abbie's call about an officer down. As he drives to the livery stable, Ichabod steps out onto the street in front of him and freezes. Brooks orders him down on his knees and Ichabod complies. Once he has been handcuffed, Brooks takes him to the police station and Abbie looks him over. She tells Brooks that Ichabod isn't the killer and describes the brand. When Ichabod overhears her description, he asks if the killer had a broad axe and describes the brand. When Abbie wonders how he knows what the killer looked like, Ichabod says that he cut off the Horseman's head.
The next day, Captain Frank Irving calls in a polygrapher to interrogate Ichabod. While Ichabod tries to take in all of the advanced technology, the polygrapher advises him to cooperate so they can release him if he's innocent. Ichabod agrees and says that he's a professor at Merton College at Oxford. He joined the British Army and fought the colonists, but switched sides when he realized the righteousness of their cause. Ichabod then worked as a spy for General George Washington. As for the Horseman, Ichabod explains that he decapitated the Horseman to stop him, but was mortally wounded. He was taken to triage where his wife Katrina worked as a civilian nurse for the Continental Army. The next thing Ichabod knew, he was in a cave in the present day. When Ichabod demands to know where he is, the polygrapher tells him that the Americans won the war 250 years ago.
Afterward, the polygrapher informs Irving and Abbie that Ichabod believes what he's saying, but it's possible to fool a machine. Irving orders Ichabod delivered to St. Gregory's for a psych evaluation, but Abbie wants to question him further. She notes that Ichabod described the killer she saw, and also that she has found one peculiar fact: Corbin's neck wound was cauterized as if someone used a heated blade. However, there were no traces of fire in the area. Abbie insists that Ichabod knows something that can help them find the killer, but Irving refuses to give her time to interrogate their prisoner. Switching tracks, the lieutenant asks for permission to take Ichabod to St. Gregory's so that she can interrogate him on the way. When she suggests that doing so could give her some closure on Corbin's death, Irving agrees.
Abbie goes to get Ichabod, who assumes that she's a former slave who has been freed. She takes him out to her squad car and Ichabod concludes that she's helping him because she has no one else to turn to. Ichabod tells Abbie that he believes what she claimed to saw, and figures that it's no coincidence that he awoke just as the Horseman started a rampage. Refusing to believe him, Abbie shoves him in the car. As they drive to St. Gregory's, Abbie tells him to direct her to the cave where he woke up. Ichabod is amused that she's disobeying orders, but Abbie points out that no one will believe him if he reports it. As they drive by the church, Ichabod catches a glimpse of Reverend Knapp out front and remembers him... from 1781, when he lay dying.
When Ichabod and Abbie investigate the cave, Ichabod finds an old Bible on the ground. He picks it up and remembers Knapp placing it on his chest in 1781. There's a bookmark indicating the Book of Revelations, the verse that tells of the Four Horsemen of the Apocalypse. Death rides a white horse, just as the Horseman did, and holds a bow in his hand. Ichabod tells Abbie that General Washington had warned him that the outcome of the American Revolution would determine the fate of everyone on Earth, and asked him to track down the Horseman. The Horseman was supposedly a mercenary working for the British, and had the brand of a bow on his hand. Abbie doesn't believe she's dealing with Biblical prophecy, but Ichabod warns her that the Horseman has returned to Sleepy Hollow to finish what it started in 1781.
As night falls, the Horseman gallops through the horses atop its stolen white stallion.
As Knapp leaves his church, shovel in hand, he hears the Horseman approaching and runs to the street. The Horseman cuts him off and advances on him, broad axe at the ready. Knapp casts a spell, animating the nearby guard chains and ordering them to attack. The Huntsman easily cuts through them with his heated blade, and advances on Knapp. The reverend vows that he'll never reveal where "it" is hidden, and the Horseman decapitates him.
Abbie hears about the radio on her police radio and drives to the church. After telling Ichabod to stay in the car, she goes over to Irving and Brooks, who are examining the corpse. While he waits, Ichabod sees a hawk land on the hood of Abbie's car and look at him. He gets out and follows it into the church's cemetery. Meanwhile, Abbie confirms that Knapp was also killed with a heated blade. Irving sees Ichabod and demands to know what's going, and Abbie explains that Ichabod was with her so he can't have killed Knapp. Unimpressed, Irving tells Abbie to get Ichabod to St. Gregory's or face suspension. As the captain walks away, Brooks advises Abbie to play along.
Ichabod discovers that the hawk has landed on a gravestone as Abbie comes over. The gravestone is in honor of Ichabod's wife, Katrina, who was burned for witchcraft in 1782. Ichabod points out that the gravestone proves his claim since he described Katrina, but Abbie doesn't believe it. When she says that she has to obey orders or risk being stuck in Sleepy Hollow, Ichabod realizes that she is planning to leave. He warns her that her fate is intertwined with his and she has to stay. Abbie walks off, refusing to accept the story of the Horseman, and says that it's happened before. Ichabod tries to find out what happened before but Abbie refuses to explain. She takes him to St. Gregory's and gets him a private cell, and Ichabod has time to consider if he really is insane. Abbie says that she knows what he's going through, and explains that she when she and her sister Jenny were in high school, they were walking through the forest when four strange white trees appeared nearby. A demonic figure started to emerge from the ground... and the sisters blacked out. When they woke up, everyone said they were crazy to the point where it drove Jenny insane. Abbie's sister has been in and out of institutes ever since. Abbie tells Ichabod that she knows what it feels like to doubt one's sanity, and Ichabod offers his condolences on her partner's death.
The next morning, Abbie sneaks into her dead partner's office and looks around. As she picks up a photo he had of her, Abbie notices a key tapped to the back. Searching the office, she discovers that it opens cabinet. Inside are files on hundreds of murders and disappearances, as well as a tape player. Abbie plays it and listens as Corbin describes how there were two covens of witches in Sleepy Hollow, one good and one evil. During the witch trials, both cults went underground, changing their names and blending into the populace. Since then, there have been hundreds of unsolved murders and disappearances along the East Coast. Among Corbin's files is one on Abbie and Jenny's encounter in the forest. The sheriff had knowledge of a similar encounter with the white trees that a farmer had in 1882. The farmer believed that the four trees represented the Four Horsemen of the Apocalypse and the demonic figure that emerged was sent to raise the Horsemen. Corbin finishes the recording by stating that he didn't know he could trust with the information he had, and that he could never figure out how to tell Abbie what he learned. As Abbie returns the files to the cabinet, Irving comes in and hides the key. She claims that she just came to look for Corbin's files and claims that she didn't find anything. The captain tells her to go home and get some rest while they do their jobs. Once Abbie leaves, Irving glances suspiciously around the room.
Ichabod wakes up in his hospital bed and realizes that he's dreaming. The bird he saw earlier is perched at the end of the bed, and then flies through the mirror and into the forest on the other side. Katrina is standing there and says that she can only reach Ichabod through her dreams. She explains that she isn't buried in the grave, and that in fact it conceals the Horseman's skull. Knapp buried it there and guarded it to prevent the others from finding it. Ichabod was brought back to life because when he decapitated the Horseman, their blood merged and the two of them became linked. Katrina's cult locked the Horseman's corpse in an iron box and threw it into the window, then buried Ichabod in the cave to protect him. When the evil coven resurrected the Horseman, the link woke Ichabod up as well.
Something moves in the surrounding forest and Katrina warns her husband that the demon is coming for her. She warns that if the Horseman recovers his skull then he will become whole again, and the other three Horsemen of the Apocalypse will then take their place on Earth... bring about the end of days. Katrina calls Ichabod the "First Witness" and tells him that the Horseman can't survive the sunrise. The demon approaches them as Katrina tells Ichabod that the Washington Bible holds the answers to all of his questions, and then orders him to wake up.
Ichabod wakes up to discover that he's been screaming in his sleep. Two orderlies restrain him and a doctor prepares to give him a sedative. Abbie arrives just in time and gives the doctor a court order releasing Ichabod into her custody. Once they're out in the hallway, Abbie tells Ichabod that they need to get out before the doctor realizes that the "court order" is a fake. They go out to the car and Ichabod explains that the Horseman is searching for its skull. Abbie held onto a map that Corbin made of the Hudson Valley in 1776, a map signed by George Washington. Corbin was trying to work out what was going on in Sleepy Hollow by noting where supernatural incidents occurred. Abbie wonders if the white trees and the demon she saw as a child are real, and Ichabod assures her that he saw them as well and that he believes her.
As the sun sets, the Horseman emerges from the river and goes to its waiting steed.
After Ichabod explains where the skull is hidden, Abbie calls Brooks on the radio and tells him to get all units to the church. Brooks warns her that if she's wrong then they'll both be in a lot of trouble, but agrees to help. When Brooks goes to his apartment, he discovers that someone has broken the lock. He goes inside, gun drawn, and finds the Horseman waiting for him. The Horseman has broken open the cabinet holding Brooks' weapons and armed itself, and Brooks tells it that he knows where its skull is hidden.
Ichabod and Abbie drive to the cemetery and dig up the false grave. Inside is the skull, sealed in a jar. Its eyes glow as the Horseman arrives. It fires on them with Brooks' semi-automatic rifle, forcing Abbie to take cover while Ichabod dives into the open grave with the jar. The Horseman advances on the grave and prepares to shoot Ichabod, and Abbie shoots it repeatedly, giving Ichabod time to attack it with a shovel. Brooks pulls up and Abbie goes to his car and tells him to get out his weapons. As she reaches into the trunk, Brooks pistol-whips her and then drags her into the back of his car, insisting that he'll protect her.
The Horseman proves too much for Ichabod, who grabs the jar and runs into the church. Meanwhile, a stunned Abbie manages to bite Brooks' hand and then grab his gun. She aims it and orders Brooks to handcuff himself to the car door. Two officers arrive and order the Horseman to surrender, but are taken aback when they realize it has no head. Before it can respond, the sun starts to come up and the Horseman's body smolders. It opens fire on the police car, demolishing it and forcing them to take cover, and then rides off ahead of the sun. Abbie runs over just as Ichabod calls to her, and the lieutenant stops the nervous officers from shooting her new ally.
Back the station, Brooks is booked and Irving tells Ichabod and Abbie that they now have enough evidence to corroborate her story. Brooks has agreed to plea bargain as long as he can do so directly to Abbie. Abbie warns her superior that they've only scratched the surface of what is going on. As Irving walks away, Ichabod asks Abbie if she's still leaving for Quantico, and she tells him that she now believes that she's supposed to stay in Sleepy Hollow.
As they go to Brooks' cell, Ichabod explains that his wife called him the First Witness. He has checked Washington's Bible, which refers to two Witnesses in the Book of Revelation. The Witnesses will come together to deal with a seven-year period of tribulation and fight the forces of Hell. Whoever wins will triumph on Judgment Day. Ichabod believes that he and Abbie are the Witnesses and that his new friend has been called to finish Corbin's work.
Brooks is sitting alone, passing easily through the walls. It tells him that it has failed and ignores Brooks' pleas for a second chance. The demon breaks his neck with a single gesture just as Abbie and Ichabod arrive. They discover that Brooks is dead and Abbie sees the demon in the mirror, walking off through the forest. As she remembers what Corbin said on the tape, the demon turns to look at her, shattering the mirror.