After being impaled by a pipe and plunging into a river at the end of the previous film, the undead "Maniac Cop" Matthew Cordell acquires a junked police cruiser and restarts his killing spree through New York City. Finding a convenience store in the middle of a robbery, he kills the clerk; the thief is subsequently killed in a shootout with police. As Cordell stalks the streets, his enemies Officers Jack Forrest and Theresa Mallory are put back on duty by Deputy Commissioner Edward Doyle, who has the two undergo a psychiatric evaluation under Officer Susan Riley. While Jack is content that Cordell is long gone and wants to go on with his life, Theresa is convinced that Cordell is still alive and plotting his revenge.
At a newsstand, Jack is stabbed through the neck by Cordell, killing him. In order to protect the memory of Commissioner Pike, the corrupt official who originally framed Cordell, the police authority refuse to inform the public of the nature of recent events. This, along with her belief that Cordell is alive and killing, prompts Theresa to appear on a talk show to inform the public about Cordell. A traffic cop is murdered by Cordell later when he was towing someone's car. The man who was having his car towed is arrested on suspicion on the cop's murder. While en route to a hotel in a taxi, Theresa is joined by Susan, and the two are attacked by Cordell, who kills the cabbie and forces Susan and Theresa off the road. After handcuffing Susan to the steering wheel of a car and sending her into the busy streets, Cordell kills Theresa by snapping her neck. Gaining control of the car, Susan crashes and is found and given medical attention.
Elsewhere, a stripper named Cheryl is attacked in her apartment by Steven Turkell, who has strangled at least six other exotic dancers. As Turkell brutalizes Cheryl, Cordell arrives, murders the two officers earlier called by Cheryl, and helps Turkell escape. Grateful for the help, Turkell befriends Cordell and takes him back to his apartment, where Cordell stays for a short while. After Cordell leaves, Turkell goes out to find another victim but is identified at a strip club by Cheryl. He is arrested and placed in a holding cell by Susan and Detective Lieutenant Sean McKinney.
Turkell taunts Susan, telling him Cordell will break him out. Turkell's assumption proves correct, as Cordell breaks into the police station and murders a total of nineteen police officers and frees Turkell and several unnamed convicts. Using Susan as a hostage, Turkell, Cordell, and another criminal named Joseph Blum hijack a prison bus and head to Sing Sing, where Turkell believes Cordell wants to free all the inmates and create an army of criminals. McKinney and Doyle follow, and McKinney convinces Doyle to reopen Cordell's case and rebury his casket with full honors on the assumption that this will appease Cordell.
Cordell bluffs his way into the prison using Blum's paperwork, and he kills a guard for his keys. Shortly after entering death row, Cordell is contacted over the prison PA system by Doyle, who admits to Cordell that he was set up and states that his case has been reopened. After hearing Doyle's announcement, Cordell abandons Turkell, Blum, and Susan and heads deeper into the prison, where he is attacked with a Molotov cocktail by the three inmates who originally mutilated and killed him. While burning, Cordell finally gets his revenge by killing the three convicts who mutilated him, only to be attacked by Turkell, who realizes Cordell used him. As Cordell and Turkell fight, the two crash through a wall, fall onto the bus below, and seemingly die when the vehicle explodes.
Sometime later, Cordell is buried with full honors alongside other fallen officers; Susan and McKinney attend his funeral. As Cordell's casket is lowered, McKinney throws Cordell's badge into the grave, leaves with Susan, and delivers a monologue about how there is a little bit of Cordell in every officer, and that every member of the force needs to know that justice and pressure are the only differences between a cop and a Maniac Cop. Then the camera slowly and eerily pans toward Cordell's casket, and suddenly, Cordell's hand unexpectedly bursts through the lid of his casket and quickly grabs his badge, as the screen cuts to black, and the credits roll.
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