On the subway to the slaughterhouse district, Jerry and Leona encounter a group of gang members harassing a passenger. The passenger pulls a gun on them and the gang members do the same, prompting several other commuters to pull their guns as well. As Jerry and Leona try to defuse an impending shootout, the predator jumps onto the roof of their car and enters it. It wades through the passengers, killing anyone who possesses a weapon.
Leona is able lead most of the passengers out of the car and to the opposite end of the train. While she does, she sees Jerry shooting at an invisible target. Jerry's bullets have no effect and he leaps at the predator with a large knife. Leona pulls an alarm that stops the train and she guides the passengers out of the platform. She walks back to the last car and finds Jerry and a couple of commuters hung upside and dead. The predator suddenly appears and grabs her.
Looking her over with it's infrared vision, it sees that she's pregnant. Harrigan arrives on the scene and sees the carnage. Jerry's body is gone and he walks down the tunnel, searching. He spots the predator ripping Jerry's skull and spinal column from his body. Harrigan chases it to street level. He steals a police car and chases it several blocks until he's stopped by Keyes' men.
Taken to a high-tech command center, Keyes explains that the predator is an alien that uses advanced weaponry. He tells Harrigan about a commando team that encountered another of these creatures in a Latin American jungle 10 years prior. Keyes says that they believe the alien can only track it's prey using infrared technology and that his team, intending to capture it and study it, will wear special suits that will insulate their body heat and make them invisible.
At the same time, they will dust the slaughterhouse with radioactive particles that will make the alien visible. Their ultimate goal is to freeze the alien with frozen nitrogen. The predator comes to the location every couple of days to eat the beef there. Keyes tells Harrigan to stay in the command center and observe. Keyes and his team move into the slaughterhouse. Their equipment functions well at first, until a couple of team members step on a creaking stair.
The predator, hearing the noise, uses a small control panel to adjust it's vision enhancer, which changes several times until it's able to see the beams from the lights the team are using. Harrigan tries to warn Keyes that they've been spotted but the team is attacked by the predator, which kills nearly all of them. One of the teams sprays a smoke detector with nitrogen, setting off the warehouse's sprinkler system.
Harrigan leaves the command center, arms himself and blows down the door just as the predator fires a blast from it's laser cannon at Keyes. Harrigan shoots at the predator, damaging its laser cannon. The alien tries to activate it's cloaking system but the water falling from the ceiling prevents from becoming invisible. Harrigan shoots the predator several times with a shotgun, blowing it onto its back.
He approaches it slowly and removes it's helmet, studying it briefly before it wakes up suddenly and throws Harrigan backwards. The predator finally corners Harrigan and is about to kill him when Keyes intervenes, trying to blast the monster back with frozen nitrogen. Keyes tells Harrigan to retreat just as the alien throws a smart disk, cutting Keyes in half. The predator retreats to the roof of the building, using a breathing mask.
It throws its large hunting spear at Harrigan and misses. Harrigan uses the spear to push the alien and himself off the building, where they both hang onto a ledge. The predator activates a timer connected to a small nuclear charge. Before the charge can go off, though, Harrigan uses the alien's smart disk to sever it's arm, deactivating the bomb. The alien falls down the side of the building and crashes into an apartment bathroom.
It uses an elaborate first aid kit to heal it's wounds and again retreats. Harrigan follows it, falling into a cavern below the building where the alien's spacecraft has been hidden. Inside the spaceship, Harrigan finds a small shrine of sorts with skulls of humans, animals and aliens. The predator once again attacks Harrigan who fights it off and kills it with its smart disk.
After it falls dead, several more predators appear and carry their fallen comrade off. The last one to leave looks over Harrigan briefly and tosses him a flintlock pistol, a trophy from a previous hunt. Engraved on the pistol is the original owner's name and the year 1715.
Harrigan hears the ship starting up and runs out to cover just before the blast from the engines fills the cavern. As Harrigan walks out of a tunnel he meets one of Keyes' assistants, who, upon seeing the haggard Harrigan, leaves him.
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