Jack uses Burt's ultrasonic watch to lure the last Graboid into eating the last Ass Blaster. The town then takes precautions to keep itself safe, since Graboid hunting is now illegal.
After successfully completing a Shrieker hunt in Argentina, Burt Gummer (Michael Gross) has returned to Perfection, the setting of the first movie, only to find that the town has been turned into a tourist attraction. Many of the original survivors, including Nancy, Mindy, Melvin, and Miguel, are still residents of Perfection, and they have been joined by Jodi, who now runs here late Uncle Walter's store, and Jack, who runs a fake Graboid hunt for tourists. During one of Jack's hunts, a real Graboid kills his assistant. Jack and the tourists barely make it back to town, where they call the government for help, much to Burt's chagrin. When the government agents arrive, they tell Burt and the townspeople that it's now illegal to kill Graboids since they are now considered endangered species. But a deal is eventually worked out that if the agents capture a Graboid for study, Burt can kill the other two.
While the agents are chasing a Graboid, Burt and Jack kill one by forcing it to slam head-first into a concrete barrier. Before they can get the other one, Burt and Jack, now joined by Jodi and Miguel , find one of the government agents. He tells them that it hatched Shriekers before it could be caught and it killed the other agents before they got away, then he dies from his wounds. The Shriekers are trapped in a canyon, but the group can't kill them because they are trapped themselves by the last Graboid, an albino one they name "El Blanco". Since albinos are naturally sterile, they know that this one will never hatch Shriekers. Once the group is finally able to get to the canyon, they find the shed skins of the Shriekers and discover that they have evolved again, and this time they can fly.
These flying Shriekers launch themselves like a rocket, and fire can come out of their rear ends, so Jodi names them Ass Blasters. One of the Ass Blasters kills Miguel, and the rest fly away. One of them flies to Perfection, and it traps Nancy and Mindy inside the store. Burt, Jack, and Jodi make their way to Burt's house to get weapons, but another Ass Blaster crashes into the house before they can get any. In order to prevent it from eating his MREs and multiply, Burt uses the fire from the Ass Blaster to blow up his house. Only then does he find out from Nancy and Mindy that these creatures actually fall asleep after eating and they have tied up the one that was in the store with them.
Burt, Jack, and Jodi make their way to the junkyard, and it's there that Jack comes up with the idea to make a potato gun and use it to launch burning arrows at the creatures to destroy them. They find the parts they need and after several close calls, the trio kill all the remaining Ass Blasters in the junkyard . On their way out of the junkyard, they are attacked by El Blanco. Burt realizes that it is following the ultrasonic sound his watch is making, but then the trio is attacked by one last Ass Blaster. A quick thinking Jack takes Burt's watch and pins it to the Ass Blaster, then El Blanco eats it, which saves their lives.
A short time later, Nancy and Mindy make a deal with Siegfried and Roy to sell them the captive Ass Blaster. Jack, who has taken a job in a nearby town, begins a relationship with Jodi, which saddens Mindy because she had a crush on him. Burt is approached by Melvin, who has been trying to sell the town to build it up, about selling his land now that he no longer has a house. Burt refuses, and tells Melvin that since El Blanco is endangered and cannot be hunted, the residents have chosen to take precautions to keep Perfection Graboid-proof, which ruins his plans for development. The movie ends with Burt stranding Melvin on a rock with El Blanco circling it.