The film picks up immediately after the end of the last film, with Marybeth Dunston (Danielle Harris) blowing off the head of Victor Crowley (Kane Hodder) with a shotgun. She walks away and comes across the bodies of Vernon and John, where she hears a somehow still alive Victor in the woods. Marybeth starts up the chainsaw and prepares for a fight, but is grabbed by Victor, whose head is bloody but reattached. Marybeth puts her arm through his bloody face, and he falls backwards onto the chainsaw, cutting him down the middle and in half. After shooting Victor's head to make sure he is dead this time, Marybeth is satisfied.
She walks back into the city, bloodied and disorientated. She walks into the Jefferson Parish Police Department, immediately having guns drawn on her. Upon discovery of the twenty to thirty bodies at Honey Island Swamp, she is placed as the prime suspect in the murders by Sheriff Fowler (Zach Galligan), even after telling him numerous times about the events of the last two films. The Sheriff heads out to the swamp with the paramedics and fire department, leaving Deputy Winslow (Robert Diago DoQui) in charge of the station until he gets back.
Amanda Fowler (Caroline Williams), the Sheriff's ex-wife, journalist and an expert about the legend of Victor Crowley, comes into the station to interview Marybeth about what happened, telling Marybeth she wants to help, otherwise Marybeth will be tried and executed for what happened at Honey Island Swamp. After retelling the events of the previous two films to Amanda, Amanda tells her that Victor Crowley is a repeater, set to relive the night he died, looking for his father and that he will keep coming back unless he gets what he wants: his father. She tells Marybeth that her father, Sampson Dunston, was the one that came up with the idea to start the fire many years ago and tried to get him to deliver Thomas Crowley's ashes to Victor over the past several years, only to be dismissed numerous times. Since he's dead and she's Sampson's bloodline, only she can put an end to Victor Crowley. Marybeth doesn't believe her, continuously declaring that she killed Victor Crowley the night before.
At Honey Island Swamp, the body of Victor Crowley is bagged and tagged and put into the ambulance boat. When the paramedic, Randy (Sean Whalen) is distracted, Victor reanimates and blows Randy's head off with a defibrillator. Deputy Hamilton (Jason Trost) goes to investigate and goes to the boat where Victor appears and kills him by hacking his head in half. Victor then kills about a dozen or so of the first response team (four of them onscreen), leaving paramedic Andrew (Parry Shen), and another paramedic alive. Victor then escapes back to his house. Back at the station, upon hearing the medical team getting killed on the radio, Amanda convinces Deputy Winslow to let Marybeth out of jail and help her save everyone at Honey Island Swamp.
Back at the swamp, in comes the SWAT team, led by Tyler Hawes (Derek Mears) and consists of five others: four armed men and one armed woman named Dougherty (Rileah Vanderbilt). Hawes takes over the operation from Fowler and leads them to the Crowley house, where an officer is killed. After he throws the corpse out of the shed, Crowley kills Elbert (Diane Ayala Goldner). Crowley ambushes two officers as the SWAT team gangs up on him and fail, as they futilely shoot Crowley as he kills all SWAT but Hawes and Dougherty. Hawes tries tackling Crowley but is in turn pinned against the shed and has his skull and spine ripped out. While Deputy Rick catches Victor's attention, Deputy Schneiderman (Cody Blue Snider) takes the opportunity to fire a rocket launcher at Crowley, but misses and hits Rick instead, killing him. The resulting explosion blows up the Crowley house, destroying it and covering Victor in the rubble. When Schneiderman begins to celebrate, Victor appears from the wreckage and throws a piece of rubble into Schneiderman's back. He then proceeds to kills Schneiderman by ripping his arms off and drowning him in a puddle. Dougherty, Andrew and the Sheriff run for it. Before running, the Sheriff manages to slow Crowley down by shooting in the chest with a handgun.
Meanwhile, Amanda has Winslow take her and Marybeth to the house of Abbott MacMullen (Sid Haig), Victor Crowley's racist long distant cousin and only living blood relative who possesses the ashes of Thomas Crowley. When he declines to give up the ashes, Amanda holds him at gunpoint and leaves with the ashes. Back at Honey Island Swamp, the other paramedic is chased by Victor Crowley when he hides behind the canoe which is revealed to be the one from the first movie. It is the canoe from the first film because there, Ben (Joel David Moore), who is now revealed to still be alive, was in there, clinging to life with his left arm ripped off. As he begs for help, Victor throws the hatchet at Ben, finally killing him. Before Victor can kill the paramedic, an alligator comes out of the swamp and pulls the paramedic into the swamp to his death.
Victor resumes chasing the Sheriff, Andrew and Dougherty and corners them in the water ambulance with Randy's corpse. They barricade themselves in and the Sheriff calls for the National Guard on the ambulance's radio, telling them they're being attacked by crazed gunmen. The National Guard tells them they'll be there in ten minutes. Just as they settle down and think everything's safe, Victor begins to saw his way through the boat wall with the gas powered belt sander. The Sheriff tells them not to move, if they try to leave, they'll get killed, while Andrew thinks they should leave while he's busy cutting through the wall. Amanda, Deputy Winslow and Marybeth arrive at the Swamp outside the burned down Crowley house. Amanda calls out for Victor, telling him they have his father. Upon hearing his ex-wife's voice, Sheriff Fowler attempts to leave, only to be grabbed by Victor and beheaded with the belt sander; his arms then move around in the air before collapsing. Andrew and Dougherty are trapped in the boat with Victor on the other side of the broken door. Dougherty attempts to slowly get the Sheriff's gun, but Victor grabs and pulls her through the hole on the door, which disembowels her. Andrew smartly remains in the boat, keeping himself out of sight of Victor.
Victor goes back to his destroyed home and finds Amanda and Deputy Winslow there but refrains from attacking when he sees the ashes. Marybeth offers Victor his father's ashes and apologizes for what her father did to him. Victor proclaims "Daddy" (his only word) upon seeing the ashes. When he approaches to take the ashes, Deputy Winslow mistakes it for Victor going to attack Marybeth, and so shoots him down, but Victor rises back up, and rips apart Winslow's chest when his back is turned. Amanda grabs the urn and rolls it back to Marybeth, telling her to try it again, as she attempts to grab Winslow's gun, but Victor grabs Amanda and rips her head off. Victor then knocks Marybeth over and impales her on a tree branch, seriously injuring her. Just when Victor picks up a machete to finish Marybeth off, Marybeth smashes the urn over Victor's head, spreading his father's ashes all over him, and causing him to collapse and melt. With the last bit of her strength, she grabs one of the SWAT team's guns and blows his remains away, finally killing Victor Crowley once and for all. The National Guard then arrives and Andrew, now free of danger, emerges from the boat and signals the helicopters. Just as the screen cuts to black, one final shot of Marybeth gasping for air is shown, leaving the audience to wonder if she will live or die.
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