A baby anaconda, captured at the end of the previous film, is being used for experiments by Peter Reysner, who creates a hybrid of the blood orchids from Borneo that enabled the anaconda to grow very large and live longer, and creates a serum for cell regeneration. After the test seemingly works for the baby Dracanaconda to regenerate, Peter burns it. When he disappears, the long anaconda escapes from the cage and kills Peter in a mine filled with blood orchids. Peter "J.D." Murdoch, a billionaire suffering from bone cancer, sends his assassin Eugene and his team of henchmen mercenaries to find Peter and the serum Peter created so that it can cure him. Dr. Amanda Hayes, the sole survivor of the previous snake attack, and two officers also go in search of Peter, determined to destroy the serum and kill the snake.
On the way, they meet Alex, a trekker who appears lost in the Romanian Carpathians, while doing a paleopathology project. When they discover the blood orchids in the mine, Amanda sets the explosives to destroy the orchids, but she and the group are attacked by the anaconda that seemingly kills both officers. Amanda is able to trick the snake into causing a cave-in that "kills" the snake however as she and Alex attempt to leave the mine, she is knocked unconscious and Alex escapes to get more help. Meanwhile, a group of explorers: Jackson, his girlfriend Heather, Heather's best friend Wendy, and brothers Patrick and Scott, get dragged into the search for the snake. Due to the serum, the anaconda can no longer die without significant damage to its internal organs and regenerates itself from the previous cave-in. Heather falls ill due to a spider bite.
The next day, the group Murdoch hires is attacked by the anaconda and it kills one of them. Alex and Amanda regroup after Amanda saves Alex from the snake and they both eventually find the explorers after the snake attacks and tears off Patrick's arm. Eugene and his henchmen eventually find Hayes and Jackson's group and capture them. When Amanda is uncooperative in their efforts to get information about the serum, Eugene shoots and kills Patrick. During this moment of confusion, Wendy tries to escape and Eugene shoots her dead, which enrages Jackson.
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